BigDataScript report: chipseq.bds

Script file /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/chipseq.bds
Program ID chipseq.bds.20170128_225755_491
Start time 2017-01-28 22:57:55
Run time 02:29:32.793
Tasks executed 26
Tasks failed 0
Tasks failed names 
 

		
  Arguments*  [-title, H4ac, -species, hg38, -fastq1, /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/RawReadsFiles/SRR1015998.fastq.gz, -ctl_fastq, /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/ENCFF001HNC.fastq.gz, -final_stage, idr, -histone, $] 

		
  System*  sge 

		
  Cpus*  -1 

		
  Exit value  0 

	

	* Values in global scope when program finished execution.





	
 Timeline 

	
	
	






	
 Task Graph 

	






	
 Parallel (threads) details 

	

    
  Thread ID      Parent           	 Tasks  

	
  thread_Root   None 	 
 chipseq.bds.20170128_225755_491/task.callpeak_macs2.macs2_rep1.line_71.id_25
chipseq.bds.20170128_225755_491/task.callpeak_macs2.macs2_rep1_pr1.line_71.id_26
chipseq.bds.20170128_225755_491/task.callpeak_macs2.macs2_rep1_pr2.line_71.id_27
chipseq.bds.20170128_225755_491/task.callpeak_naive_overlap.naive_overlap_thresh.line_59.id_28
chipseq.bds.20170128_225755_491/task.callpeak_naive_overlap.naive_overlap_thresh.line_59.id_29
chipseq.bds.20170128_225755_491/task.callpeak_naive_overlap.naive_overlap_thresh.line_59.id_30
chipseq.bds.20170128_225755_491/task.callpeak_blacklist_filter.blacklist_filter_peak_1.line_27.id_31
chipseq.bds.20170128_225755_491/task.report.peak2hammock.line_412.id_32
chipseq.bds.20170128_225755_491/task.report.peak2hammock.line_412.id_33
chipseq.bds.20170128_225755_491/task.graphviz.report.line_97.id_34
chipseq.bds.20170128_225755_491/task.report.pdf2png.line_379.id_39
 
 		 

	
  thread_41   thread_Root 	 
 chipseq.bds.20170128_225755_491_parallel_41/task.align_bwa.bwa_aln_rep1.line_111.id_11
chipseq.bds.20170128_225755_491_parallel_41/task.align_bwa.bwa_sam_rep1.line_143.id_13
chipseq.bds.20170128_225755_491_parallel_41/task.postalign_bam.dedup_bam_1_rep1.line_95.id_18
chipseq.bds.20170128_225755_491_parallel_41/task.postalign_bam.markdup_bam_picard_rep1.line_348.id_19
chipseq.bds.20170128_225755_491_parallel_41/task.postalign_bam.dedup_bam_2_rep1.line_144.id_20
chipseq.bds.20170128_225755_491_parallel_41/task.postalign_bam.bam_to_tag_rep1.line_505.id_21
chipseq.bds.20170128_225755_491_parallel_41/task.postalign_bed.subsample_tag_rep1.line_45.id_22
chipseq.bds.20170128_225755_491_parallel_41/task.postalign_bed.spr_rep1.line_255.id_23
chipseq.bds.20170128_225755_491_parallel_41/task.postalign_bed.xcor_rep1.line_212.id_24
 
 		 

	
  thread_42   thread_Root 	 
 chipseq.bds.20170128_225755_491_parallel_42/task.align_bwa.bwa_aln_ctl1.line_111.id_10
chipseq.bds.20170128_225755_491_parallel_42/task.align_bwa.bwa_sam_ctl1.line_143.id_12
chipseq.bds.20170128_225755_491_parallel_42/task.postalign_bam.dedup_bam_1_ctl1.line_95.id_14
chipseq.bds.20170128_225755_491_parallel_42/task.postalign_bam.markdup_bam_picard_ctl1.line_348.id_15
chipseq.bds.20170128_225755_491_parallel_42/task.postalign_bam.dedup_bam_2_ctl1.line_144.id_16
chipseq.bds.20170128_225755_491_parallel_42/task.postalign_bam.bam_to_tag_ctl1.line_505.id_17
 
 		 

	






	
 Task details 

	

    
  Task              Execution              Time   Dependencies       Task program, Errors, StdOut / StdErr  

    
  
 
  Num   1  
 
  ID   task.align_bwa.bwa_aln_ctl1.line_111.id_10  
 
  Name   bwa_aln ctl1 
 
  Thread   thread_42  
 
  PID   35882  
 
 		  
 
  OK   true   
 
  Exit Code   0   
 
  Retries    
 
  State   FINISHED  
 
  Dep.   OK  
 
  Cpus    2 
 
  Mem    
 
 		  
 
  Start   2017-01-28 22:57:57  
 
  End   2017-01-28 23:17:44  
 
  Elapsed   00:19:47  
 
  Timeout  00:00:-1 
 
  Wall Timeout   100 days 
 
 		  
 
  Input files  /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/ENCFF001HNC.fastq.gz
   
 
  Output files   /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H4ac/out/align/ctl1/ENCFF001HNC.sai
  
 
  Dependencies     
 
 		  
 
# SYS command. line 113

 if [[ -f $(which conda) && $(conda env list | grep aquas_chipseq | wc -l) != "0" ]]; then source activate aquas_chipseq; sleep 5; fi;  export PATH=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/.:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/modules:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/utils:${PATH}:/bin:/usr/bin:/usr/local/bin:${HOME}/.bds; set -o pipefail; STARTTIME=$(date +%s); renice -n 10 $$

# SYS command. line 116

 bwa aln -q 5 -l 32 -k 2 -t 2 /mnt/data/bds_pipeline_genome_data/hg38/bwa_index/GRCh38.p3.genome.fa /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/ENCFF001HNC.fastq.gz > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H4ac/out/align/ctl1/ENCFF001HNC.sai

# SYS command. line 118

 TASKTIME=$[$(date +%s)-${STARTTIME}]; if [ ${TASKTIME} -lt 60 ]; then echo "Waiting for $[60-${TASKTIME}] seconds."; sleep $[60-${TASKTIME}]; fi
 
 
   
--------------------Stdout--------------------
4968 (process ID) old priority 0, new priority 10

 
--------------------Stderr--------------------
[bwa_aln] 17bp reads: max_diff = 2
[bwa_aln] 38bp reads: max_diff = 3
[bwa_aln] 64bp reads: max_diff = 4
[bwa_aln] 93bp reads: max_diff = 5
[bwa_aln] 124bp reads: max_diff = 6
[bwa_aln] 157bp reads: max_diff = 7
[bwa_aln] 190bp reads: max_diff = 8
[bwa_aln] 225bp reads: max_diff = 9
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 30.53 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 262144 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 36.51 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 524288 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 33.05 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 786432 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 32.20 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 1048576 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 31.59 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 1310720 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 32.72 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 1572864 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 33.71 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 1835008 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 33.12 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 2097152 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 31.70 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 2359296 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 32.30 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 2621440 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 31.79 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 2883584 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 33.30 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 3145728 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 33.10 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 3407872 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 32.49 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 3670016 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 32.47 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 3932160 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 32.70 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 4194304 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 31.93 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 4456448 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 32.77 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 4718592 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 32.07 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 4980736 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 32.46 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 5242880 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 32.65 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 5505024 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 34.34 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 5767168 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 32.52 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 6029312 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 32.88 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 6291456 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 32.87 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 6553600 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 32.10 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 6815744 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 32.14 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 7077888 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 32.55 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 7340032 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 30.83 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 7602176 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 30.81 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 7864320 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 30.53 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 8126464 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 31.37 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 8388608 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 32.35 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 8650752 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 31.86 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 8912896 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 31.96 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 9175040 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 32.31 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 9437184 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 31.92 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 9699328 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 31.48 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 9961472 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 31.09 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 10223616 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 31.85 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 10485760 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 31.55 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 10747904 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 31.70 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 11010048 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 32.02 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 11272192 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 30.59 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 11534336 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 32.13 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 11796480 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 31.06 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 12058624 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 31.74 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 12320768 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 31.39 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 12582912 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 32.03 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 12845056 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 32.28 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 13107200 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 30.76 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 13369344 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 32.30 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 13631488 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 31.21 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 13893632 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 31.87 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 14155776 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 31.90 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 14417920 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 32.75 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 14680064 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 31.42 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 14942208 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 31.72 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 15204352 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 31.79 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 15466496 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 30.45 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 15728640 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 31.18 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 15990784 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 31.44 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 16252928 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 32.08 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 16515072 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 31.53 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 16777216 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 30.41 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 17039360 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 30.74 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 17301504 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 30.16 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 17560427 sequences have been processed.
[main] Version: 0.7.13-r1126
[main] CMD: bwa aln -q 5 -l 32 -k 2 -t 2 /mnt/data/bds_pipeline_genome_data/hg38/bwa_index/GRCh38.p3.genome.fa /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/ENCFF001HNC.fastq.gz
[main] Real time: 1176.717 sec; CPU: 2240.880 sec

 
 		 

    
  
 
  Num   2  
 
  ID   task.align_bwa.bwa_aln_rep1.line_111.id_11  
 
  Name   bwa_aln rep1 
 
  Thread   thread_41  
 
  PID   35883  
 
 		  
 
  OK   true   
 
  Exit Code   0   
 
  Retries    
 
  State   FINISHED  
 
  Dep.   OK  
 
  Cpus    2 
 
  Mem    
 
 		  
 
  Start   2017-01-28 22:57:57  
 
  End   2017-01-28 23:31:34  
 
  Elapsed   00:33:37  
 
  Timeout  00:00:-1 
 
  Wall Timeout   100 days 
 
 		  
 
  Input files  /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/RawReadsFiles/SRR1015998.fastq.gz
   
 
  Output files   /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H4ac/out/align/rep1/SRR1015998.sai
  
 
  Dependencies     
 
 		  
 
# SYS command. line 113

 if [[ -f $(which conda) && $(conda env list | grep aquas_chipseq | wc -l) != "0" ]]; then source activate aquas_chipseq; sleep 5; fi;  export PATH=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/.:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/modules:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/utils:${PATH}:/bin:/usr/bin:/usr/local/bin:${HOME}/.bds; set -o pipefail; STARTTIME=$(date +%s); renice -n 10 $$

# SYS command. line 116

 bwa aln -q 5 -l 32 -k 2 -t 2 /mnt/data/bds_pipeline_genome_data/hg38/bwa_index/GRCh38.p3.genome.fa /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/RawReadsFiles/SRR1015998.fastq.gz > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H4ac/out/align/rep1/SRR1015998.sai

# SYS command. line 118

 TASKTIME=$[$(date +%s)-${STARTTIME}]; if [ ${TASKTIME} -lt 60 ]; then echo "Waiting for $[60-${TASKTIME}] seconds."; sleep $[60-${TASKTIME}]; fi
 
 
   
--------------------Stdout--------------------
4967 (process ID) old priority 0, new priority 10

 
--------------------Stderr--------------------
[bwa_aln] 17bp reads: max_diff = 2
[bwa_aln] 38bp reads: max_diff = 3
[bwa_aln] 64bp reads: max_diff = 4
[bwa_aln] 93bp reads: max_diff = 5
[bwa_aln] 124bp reads: max_diff = 6
[bwa_aln] 157bp reads: max_diff = 7
[bwa_aln] 190bp reads: max_diff = 8
[bwa_aln] 225bp reads: max_diff = 9
[bwa_read_seq] 0.9% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 47.51 sec
[bwa_aln_core] write to the disk... 0.08 sec
[bwa_aln_core] 262144 sequences have been processed.
[bwa_read_seq] 0.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 38.95 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 524288 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 36.18 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 786432 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 35.91 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 1048576 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 35.11 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 1310720 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 34.94 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 1572864 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 34.06 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 1835008 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 33.66 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 2097152 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 33.94 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 2359296 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 32.79 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 2621440 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 34.16 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 2883584 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 34.57 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 3145728 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 34.64 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 3407872 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 33.67 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 3670016 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 34.35 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 3932160 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 33.36 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 4194304 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 35.27 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 4456448 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 33.40 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 4718592 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 33.77 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 4980736 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 33.86 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 5242880 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 34.14 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 5505024 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 33.34 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 5767168 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 35.39 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 6029312 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 34.73 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 6291456 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 33.91 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 6553600 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 33.66 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 6815744 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 34.05 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 7077888 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 32.97 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 7340032 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 32.77 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 7602176 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 34.36 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 7864320 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 34.87 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 8126464 sequences have been processed.
[bwa_read_seq] 0.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 33.48 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 8388608 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 34.19 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 8650752 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 33.60 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 8912896 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 33.41 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 9175040 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 32.70 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 9437184 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 33.39 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 9699328 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 33.29 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 9961472 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 34.69 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 10223616 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 33.03 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 10485760 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 33.40 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 10747904 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 34.49 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 11010048 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 37.11 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 11272192 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 35.43 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 11534336 sequences have been processed.
[bwa_read_seq] 0.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 34.60 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 11796480 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 33.50 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 12058624 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 38.02 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 12320768 sequences have been processed.
[bwa_read_seq] 0.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 35.16 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 12582912 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 55.91 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 12845056 sequences have been processed.
[bwa_read_seq] 0.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 41.45 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 13107200 sequences have been processed.
[bwa_read_seq] 0.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 43.55 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 13369344 sequences have been processed.
[bwa_read_seq] 0.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 50.32 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 13631488 sequences have been processed.
[bwa_read_seq] 0.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 44.76 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 13893632 sequences have been processed.
[bwa_read_seq] 0.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 37.38 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 14155776 sequences have been processed.
[bwa_read_seq] 0.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 33.37 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 14417920 sequences have been processed.
[bwa_read_seq] 0.4% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 34.51 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 14680064 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 34.17 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 14942208 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 36.76 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 15204352 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 34.48 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 15466496 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 33.73 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 15728640 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 43.18 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 15990784 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 39.81 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 16252928 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 33.71 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 16515072 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 36.09 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 16777216 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 36.58 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 17039360 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 37.75 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 17301504 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 37.30 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 17563648 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 37.12 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 17825792 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 38.61 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 18087936 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 36.27 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 18350080 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 37.21 sec
[bwa_aln_core] write to the disk... 0.08 sec
[bwa_aln_core] 18612224 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 36.33 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 18874368 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 37.41 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 19136512 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 36.73 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 19398656 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 37.22 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 19660800 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 34.91 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 19922944 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 35.94 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 20185088 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 34.46 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 20447232 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 34.50 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 20709376 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 33.23 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 20971520 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 34.64 sec
[bwa_aln_core] write to the disk... 0.08 sec
[bwa_aln_core] 21233664 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 35.33 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 21495808 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 36.01 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 21757952 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 34.02 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 22020096 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 35.36 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 22282240 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 34.41 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 22544384 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 34.92 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 22806528 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 35.85 sec
[bwa_aln_core] write to the disk... 0.08 sec
[bwa_aln_core] 23068672 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 36.23 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 23330816 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 35.26 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 23592960 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 33.98 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 23855104 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 33.98 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 24117248 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 34.22 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 24379392 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 34.54 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 24641536 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 34.55 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 24903680 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 34.41 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 25165824 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 34.85 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 25427968 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 35.73 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 25690112 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 34.80 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 25952256 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 33.14 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 26214400 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 33.30 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 26476544 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 34.23 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 26738688 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 33.97 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 27000832 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 33.18 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 27262976 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 2.48 sec
[bwa_aln_core] write to the disk... 0.00 sec
[bwa_aln_core] 27277223 sequences have been processed.
[main] Version: 0.7.13-r1126
[main] CMD: bwa aln -q 5 -l 32 -k 2 -t 2 /mnt/data/bds_pipeline_genome_data/hg38/bwa_index/GRCh38.p3.genome.fa /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/RawReadsFiles/SRR1015998.fastq.gz
[main] Real time: 2006.915 sec; CPU: 3843.868 sec

 
 		 

    
  
 
  Num   3  
 
  ID   task.align_bwa.bwa_sam_ctl1.line_143.id_12  
 
  Name   bwa_sam ctl1 
 
  Thread   thread_42  
 
  PID   35898  
 
 		  
 
  OK   true   
 
  Exit Code   0   
 
  Retries    
 
  State   FINISHED  
 
  Dep.   OK  
 
  Cpus    2 
 
  Mem    
 
 		  
 
  Start   2017-01-28 23:17:46  
 
  End   2017-01-29 00:07:09  
 
  Elapsed   00:49:23  
 
  Timeout  00:00:-1 
 
  Wall Timeout   100 days 
 
 		  
 
  Input files  /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/ENCFF001HNC.fastq.gz
/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H4ac/out/align/ctl1/ENCFF001HNC.sai
   
 
  Output files   /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H4ac/out/align/ctl1/ENCFF001HNC.bam
/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H4ac/out/qc/ctl1/ENCFF001HNC.flagstat.qc
  
 
  Dependencies     
 
 		  
 
# SYS command. line 145

 if [[ -f $(which conda) && $(conda env list | grep aquas_chipseq | wc -l) != "0" ]]; then source activate aquas_chipseq; sleep 5; fi;  export PATH=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/.:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/modules:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/utils:${PATH}:/bin:/usr/bin:/usr/local/bin:${HOME}/.bds; set -o pipefail; STARTTIME=$(date +%s); renice -n 10 $$

# SYS command. line 150

 bwa samse /mnt/data/bds_pipeline_genome_data/hg38/bwa_index/GRCh38.p3.genome.fa /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H4ac/out/align/ctl1/ENCFF001HNC.sai /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/ENCFF001HNC.fastq.gz | samtools view -Su /dev/stdin \
			| sambamba sort -t 2 /dev/stdin -o /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H4ac/out/align/ctl1/ENCFF001HNC.bam

# SYS command. line 152

 sambamba flagstat -t 2 /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H4ac/out/align/ctl1/ENCFF001HNC.bam > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H4ac/out/qc/ctl1/ENCFF001HNC.flagstat.qc

# SYS command. line 154

 TASKTIME=$[$(date +%s)-${STARTTIME}]; if [ ${TASKTIME} -lt 60 ]; then echo "Waiting for $[60-${TASKTIME}] seconds."; sleep $[60-${TASKTIME}]; fi
 
 
   
--------------------Stdout--------------------
5715 (process ID) old priority 0, new priority 10

 
--------------------Stderr--------------------
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 45.51 sec
[bwa_aln_core] refine gapped alignments... 7.34 sec
[bwa_aln_core] print alignments... [samopen] SAM header is present: 493 sequences.
0.65 sec
[bwa_aln_core] 262144 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 33.09 sec
[bwa_aln_core] refine gapped alignments... 5.10 sec
[bwa_aln_core] print alignments... 0.64 sec
[bwa_aln_core] 524288 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 32.10 sec
[bwa_aln_core] refine gapped alignments... 5.16 sec
[bwa_aln_core] print alignments... 0.59 sec
[bwa_aln_core] 786432 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 32.23 sec
[bwa_aln_core] refine gapped alignments... 5.19 sec
[bwa_aln_core] print alignments... 0.71 sec
[bwa_aln_core] 1048576 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 33.28 sec
[bwa_aln_core] refine gapped alignments... 5.19 sec
[bwa_aln_core] print alignments... 0.55 sec
[bwa_aln_core] 1310720 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 32.49 sec
[bwa_aln_core] refine gapped alignments... 5.06 sec
[bwa_aln_core] print alignments... 0.37 sec
[bwa_aln_core] 1572864 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 25.49 sec
[bwa_aln_core] refine gapped alignments... 5.15 sec
[bwa_aln_core] print alignments... 0.41 sec
[bwa_aln_core] 1835008 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 32.03 sec
[bwa_aln_core] refine gapped alignments... 5.20 sec
[bwa_aln_core] print alignments... 0.37 sec
[bwa_aln_core] 2097152 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 32.39 sec
[bwa_aln_core] refine gapped alignments... 5.31 sec
[bwa_aln_core] print alignments... 0.44 sec
[bwa_aln_core] 2359296 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 32.03 sec
[bwa_aln_core] refine gapped alignments... 5.13 sec
[bwa_aln_core] print alignments... 0.36 sec
[bwa_aln_core] 2621440 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 32.12 sec
[bwa_aln_core] refine gapped alignments... 5.20 sec
[bwa_aln_core] print alignments... 0.47 sec
[bwa_aln_core] 2883584 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 31.81 sec
[bwa_aln_core] refine gapped alignments... 5.17 sec
[bwa_aln_core] print alignments... 0.33 sec
[bwa_aln_core] 3145728 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 31.99 sec
[bwa_aln_core] refine gapped alignments... 5.18 sec
[bwa_aln_core] print alignments... 0.47 sec
[bwa_aln_core] 3407872 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 31.36 sec
[bwa_aln_core] refine gapped alignments... 5.20 sec
[bwa_aln_core] print alignments... 0.35 sec
[bwa_aln_core] 3670016 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 31.83 sec
[bwa_aln_core] refine gapped alignments... 5.14 sec
[bwa_aln_core] print alignments... 0.43 sec
[bwa_aln_core] 3932160 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 31.89 sec
[bwa_aln_core] refine gapped alignments... 5.13 sec
[bwa_aln_core] print alignments... 0.40 sec
[bwa_aln_core] 4194304 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 31.92 sec
[bwa_aln_core] refine gapped alignments... 5.13 sec
[bwa_aln_core] print alignments... 0.39 sec
[bwa_aln_core] 4456448 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 31.57 sec
[bwa_aln_core] refine gapped alignments... 5.18 sec
[bwa_aln_core] print alignments... 0.31 sec
[bwa_aln_core] 4718592 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 31.51 sec
[bwa_aln_core] refine gapped alignments... 5.11 sec
[bwa_aln_core] print alignments... 0.51 sec
[bwa_aln_core] 4980736 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 29.59 sec
[bwa_aln_core] refine gapped alignments... 5.33 sec
[bwa_aln_core] print alignments... 0.42 sec
[bwa_aln_core] 5242880 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 32.40 sec
[bwa_aln_core] refine gapped alignments... 5.15 sec
[bwa_aln_core] print alignments... 0.47 sec
[bwa_aln_core] 5505024 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 28.88 sec
[bwa_aln_core] refine gapped alignments... 5.10 sec
[bwa_aln_core] print alignments... 0.38 sec
[bwa_aln_core] 5767168 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 32.12 sec
[bwa_aln_core] refine gapped alignments... 5.22 sec
[bwa_aln_core] print alignments... 0.42 sec
[bwa_aln_core] 6029312 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 32.09 sec
[bwa_aln_core] refine gapped alignments... 5.17 sec
[bwa_aln_core] print alignments... 0.42 sec
[bwa_aln_core] 6291456 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 31.87 sec
[bwa_aln_core] refine gapped alignments... 5.32 sec
[bwa_aln_core] print alignments... 0.40 sec
[bwa_aln_core] 6553600 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 31.78 sec
[bwa_aln_core] refine gapped alignments... 5.15 sec
[bwa_aln_core] print alignments... 0.34 sec
[bwa_aln_core] 6815744 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 31.16 sec
[bwa_aln_core] refine gapped alignments... 5.20 sec
[bwa_aln_core] print alignments... 0.40 sec
[bwa_aln_core] 7077888 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 31.83 sec
[bwa_aln_core] refine gapped alignments... 5.09 sec
[bwa_aln_core] print alignments... 0.57 sec
[bwa_aln_core] 7340032 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 29.06 sec
[bwa_aln_core] refine gapped alignments... 5.12 sec
[bwa_aln_core] print alignments... 0.50 sec
[bwa_aln_core] 7602176 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 32.12 sec
[bwa_aln_core] refine gapped alignments... 4.96 sec
[bwa_aln_core] print alignments... 0.37 sec
[bwa_aln_core] 7864320 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 32.29 sec
[bwa_aln_core] refine gapped alignments... 5.19 sec
[bwa_aln_core] print alignments... 0.49 sec
[bwa_aln_core] 8126464 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 35.99 sec
[bwa_aln_core] refine gapped alignments... 1.31 sec
[bwa_aln_core] print alignments... 0.43 sec
[bwa_aln_core] 8388608 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 38.78 sec
[bwa_aln_core] refine gapped alignments... 7.14 sec
[bwa_aln_core] print alignments... 0.58 sec
[bwa_aln_core] 8650752 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 41.87 sec
[bwa_aln_core] refine gapped alignments... 7.24 sec
[bwa_aln_core] print alignments... 0.53 sec
[bwa_aln_core] 8912896 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 42.60 sec
[bwa_aln_core] refine gapped alignments... 4.98 sec
[bwa_aln_core] print alignments... 0.65 sec
[bwa_aln_core] 9175040 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 39.80 sec
[bwa_aln_core] refine gapped alignments... 7.13 sec
[bwa_aln_core] print alignments... 0.45 sec
[bwa_aln_core] 9437184 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 43.29 sec
[bwa_aln_core] refine gapped alignments... 7.28 sec
[bwa_aln_core] print alignments... 0.64 sec
[bwa_aln_core] 9699328 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 40.89 sec
[bwa_aln_core] refine gapped alignments... 7.63 sec
[bwa_aln_core] print alignments... 0.39 sec
[bwa_aln_core] 9961472 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 41.96 sec
[bwa_aln_core] refine gapped alignments... 7.39 sec
[bwa_aln_core] print alignments... 0.49 sec
[bwa_aln_core] 10223616 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 41.29 sec
[bwa_aln_core] refine gapped alignments... 7.15 sec
[bwa_aln_core] print alignments... 0.67 sec
[bwa_aln_core] 10485760 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 42.58 sec
[bwa_aln_core] refine gapped alignments... 6.94 sec
[bwa_aln_core] print alignments... 0.71 sec
[bwa_aln_core] 10747904 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 42.34 sec
[bwa_aln_core] refine gapped alignments... 7.24 sec
[bwa_aln_core] print alignments... 0.64 sec
[bwa_aln_core] 11010048 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 42.09 sec
[bwa_aln_core] refine gapped alignments... 7.23 sec
[bwa_aln_core] print alignments... 0.68 sec
[bwa_aln_core] 11272192 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 42.67 sec
[bwa_aln_core] refine gapped alignments... 6.13 sec
[bwa_aln_core] print alignments... 0.61 sec
[bwa_aln_core] 11534336 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 42.60 sec
[bwa_aln_core] refine gapped alignments... 7.49 sec
[bwa_aln_core] print alignments... 0.35 sec
[bwa_aln_core] 11796480 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 41.56 sec
[bwa_aln_core] refine gapped alignments... 6.57 sec
[bwa_aln_core] print alignments... 0.44 sec
[bwa_aln_core] 12058624 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 42.00 sec
[bwa_aln_core] refine gapped alignments... 7.20 sec
[bwa_aln_core] print alignments... 0.41 sec
[bwa_aln_core] 12320768 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 40.12 sec
[bwa_aln_core] refine gapped alignments... 7.16 sec
[bwa_aln_core] print alignments... 0.33 sec
[bwa_aln_core] 12582912 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 42.29 sec
[bwa_aln_core] refine gapped alignments... 7.01 sec
[bwa_aln_core] print alignments... 0.49 sec
[bwa_aln_core] 12845056 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 34.23 sec
[bwa_aln_core] refine gapped alignments... 5.09 sec
[bwa_aln_core] print alignments... 0.42 sec
[bwa_aln_core] 13107200 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 31.12 sec
[bwa_aln_core] refine gapped alignments... 5.20 sec
[bwa_aln_core] print alignments... 0.40 sec
[bwa_aln_core] 13369344 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 30.84 sec
[bwa_aln_core] refine gapped alignments... 5.13 sec
[bwa_aln_core] print alignments... 0.43 sec
[bwa_aln_core] 13631488 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 30.78 sec
[bwa_aln_core] refine gapped alignments... 5.24 sec
[bwa_aln_core] print alignments... 0.36 sec
[bwa_aln_core] 13893632 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 30.84 sec
[bwa_aln_core] refine gapped alignments... 5.08 sec
[bwa_aln_core] print alignments... 0.33 sec
[bwa_aln_core] 14155776 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 31.58 sec
[bwa_aln_core] refine gapped alignments... 4.81 sec
[bwa_aln_core] print alignments... 0.33 sec
[bwa_aln_core] 14417920 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 31.34 sec
[bwa_aln_core] refine gapped alignments... 5.09 sec
[bwa_aln_core] print alignments... 0.37 sec
[bwa_aln_core] 14680064 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 31.12 sec
[bwa_aln_core] refine gapped alignments... 4.16 sec
[bwa_aln_core] print alignments... 0.32 sec
[bwa_aln_core] 14942208 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 31.46 sec
[bwa_aln_core] refine gapped alignments... 4.29 sec
[bwa_aln_core] print alignments... 0.32 sec
[bwa_aln_core] 15204352 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 31.50 sec
[bwa_aln_core] refine gapped alignments... 4.21 sec
[bwa_aln_core] print alignments... 0.41 sec
[bwa_aln_core] 15466496 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 31.09 sec
[bwa_aln_core] refine gapped alignments... 4.23 sec
[bwa_aln_core] print alignments... 0.32 sec
[bwa_aln_core] 15728640 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 31.78 sec
[bwa_aln_core] refine gapped alignments... 4.43 sec
[bwa_aln_core] print alignments... 0.33 sec
[bwa_aln_core] 15990784 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 31.03 sec
[bwa_aln_core] refine gapped alignments... 4.20 sec
[bwa_aln_core] print alignments... 0.42 sec
[bwa_aln_core] 16252928 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 30.95 sec
[bwa_aln_core] refine gapped alignments... 5.19 sec
[bwa_aln_core] print alignments... 0.33 sec
[bwa_aln_core] 16515072 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 31.76 sec
[bwa_aln_core] refine gapped alignments... 4.51 sec
[bwa_aln_core] print alignments... 0.35 sec
[bwa_aln_core] 16777216 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 30.91 sec
[bwa_aln_core] refine gapped alignments... 4.88 sec
[bwa_aln_core] print alignments... 0.35 sec
[bwa_aln_core] 17039360 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 31.25 sec
[bwa_aln_core] refine gapped alignments... 4.20 sec
[bwa_aln_core] print alignments... 0.40 sec
[bwa_aln_core] 17301504 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 30.89 sec
[bwa_aln_core] refine gapped alignments... 5.12 sec
[bwa_aln_core] print alignments... 0.43 sec
[bwa_aln_core] 17560427 sequences have been processed.
[main] Version: 0.7.13-r1126
[main] CMD: bwa samse /mnt/data/bds_pipeline_genome_data/hg38/bwa_index/GRCh38.p3.genome.fa /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H4ac/out/align/ctl1/ENCFF001HNC.sai /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/ENCFF001HNC.fastq.gz
[main] Real time: 2803.211 sec; CPU: 2749.236 sec

 
 		 

    
  
 
  Num   4  
 
  ID   task.align_bwa.bwa_sam_rep1.line_143.id_13  
 
  Name   bwa_sam rep1 
 
  Thread   thread_41  
 
  PID   35905  
 
 		  
 
  OK   true   
 
  Exit Code   0   
 
  Retries    
 
  State   FINISHED  
 
  Dep.   OK  
 
  Cpus    2 
 
  Mem    
 
 		  
 
  Start   2017-01-28 23:31:35  
 
  End   2017-01-29 00:38:38  
 
  Elapsed   01:07:02  
 
  Timeout  00:00:-1 
 
  Wall Timeout   100 days 
 
 		  
 
  Input files  /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/RawReadsFiles/SRR1015998.fastq.gz
/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H4ac/out/align/rep1/SRR1015998.sai
   
 
  Output files   /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H4ac/out/align/rep1/SRR1015998.bam
/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H4ac/out/qc/rep1/SRR1015998.flagstat.qc
  
 
  Dependencies     
 
 		  
 
# SYS command. line 145

 if [[ -f $(which conda) && $(conda env list | grep aquas_chipseq | wc -l) != "0" ]]; then source activate aquas_chipseq; sleep 5; fi;  export PATH=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/.:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/modules:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/utils:${PATH}:/bin:/usr/bin:/usr/local/bin:${HOME}/.bds; set -o pipefail; STARTTIME=$(date +%s); renice -n 10 $$

# SYS command. line 150

 bwa samse /mnt/data/bds_pipeline_genome_data/hg38/bwa_index/GRCh38.p3.genome.fa /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H4ac/out/align/rep1/SRR1015998.sai /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/RawReadsFiles/SRR1015998.fastq.gz | samtools view -Su /dev/stdin \
			| sambamba sort -t 2 /dev/stdin -o /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H4ac/out/align/rep1/SRR1015998.bam

# SYS command. line 152

 sambamba flagstat -t 2 /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H4ac/out/align/rep1/SRR1015998.bam > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H4ac/out/qc/rep1/SRR1015998.flagstat.qc

# SYS command. line 154

 TASKTIME=$[$(date +%s)-${STARTTIME}]; if [ ${TASKTIME} -lt 60 ]; then echo "Waiting for $[60-${TASKTIME}] seconds."; sleep $[60-${TASKTIME}]; fi
 
 
   
--------------------Stdout--------------------
6192 (process ID) old priority 0, new priority 10

 
--------------------Stderr--------------------
[bwa_read_seq] 0.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 30.60 sec
[bwa_aln_core] refine gapped alignments... 1.36 sec
[bwa_aln_core] print alignments... [samopen] SAM header is present: 493 sequences.
0.55 sec
[bwa_aln_core] 262144 sequences have been processed.
[bwa_read_seq] 0.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 28.57 sec
[bwa_aln_core] refine gapped alignments... 2.12 sec
[bwa_aln_core] print alignments... 0.52 sec
[bwa_aln_core] 524288 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 29.04 sec
[bwa_aln_core] refine gapped alignments... 2.47 sec
[bwa_aln_core] print alignments... 0.62 sec
[bwa_aln_core] 786432 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 28.91 sec
[bwa_aln_core] refine gapped alignments... 2.32 sec
[bwa_aln_core] print alignments... 0.47 sec
[bwa_aln_core] 1048576 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 28.85 sec
[bwa_aln_core] refine gapped alignments... 2.64 sec
[bwa_aln_core] print alignments... 0.49 sec
[bwa_aln_core] 1310720 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 29.19 sec
[bwa_aln_core] refine gapped alignments... 2.52 sec
[bwa_aln_core] print alignments... 0.53 sec
[bwa_aln_core] 1572864 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 29.83 sec
[bwa_aln_core] refine gapped alignments... 2.37 sec
[bwa_aln_core] print alignments... 0.51 sec
[bwa_aln_core] 1835008 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 29.15 sec
[bwa_aln_core] refine gapped alignments... 4.90 sec
[bwa_aln_core] print alignments... 0.51 sec
[bwa_aln_core] 2097152 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 30.74 sec
[bwa_aln_core] refine gapped alignments... 2.71 sec
[bwa_aln_core] print alignments... 0.31 sec
[bwa_aln_core] 2359296 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 29.75 sec
[bwa_aln_core] refine gapped alignments... 5.07 sec
[bwa_aln_core] print alignments... 0.45 sec
[bwa_aln_core] 2621440 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 32.63 sec
[bwa_aln_core] refine gapped alignments... 3.47 sec
[bwa_aln_core] print alignments... 0.40 sec
[bwa_aln_core] 2883584 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 30.78 sec
[bwa_aln_core] refine gapped alignments... 4.17 sec
[bwa_aln_core] print alignments... 0.55 sec
[bwa_aln_core] 3145728 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 27.62 sec
[bwa_aln_core] refine gapped alignments... 5.01 sec
[bwa_aln_core] print alignments... 0.51 sec
[bwa_aln_core] 3407872 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 31.55 sec
[bwa_aln_core] refine gapped alignments... 5.67 sec
[bwa_aln_core] print alignments... 0.59 sec
[bwa_aln_core] 3670016 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 32.13 sec
[bwa_aln_core] refine gapped alignments... 5.17 sec
[bwa_aln_core] print alignments... 0.55 sec
[bwa_aln_core] 3932160 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 31.34 sec
[bwa_aln_core] refine gapped alignments... 4.64 sec
[bwa_aln_core] print alignments... 0.55 sec
[bwa_aln_core] 4194304 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 32.17 sec
[bwa_aln_core] refine gapped alignments... 4.21 sec
[bwa_aln_core] print alignments... 0.47 sec
[bwa_aln_core] 4456448 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 31.29 sec
[bwa_aln_core] refine gapped alignments... 4.38 sec
[bwa_aln_core] print alignments... 0.54 sec
[bwa_aln_core] 4718592 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 30.93 sec
[bwa_aln_core] refine gapped alignments... 4.73 sec
[bwa_aln_core] print alignments... 0.54 sec
[bwa_aln_core] 4980736 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 31.70 sec
[bwa_aln_core] refine gapped alignments... 4.78 sec
[bwa_aln_core] print alignments... 0.49 sec
[bwa_aln_core] 5242880 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 32.61 sec
[bwa_aln_core] refine gapped alignments... 4.46 sec
[bwa_aln_core] print alignments... 0.40 sec
[bwa_aln_core] 5505024 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 33.82 sec
[bwa_aln_core] refine gapped alignments... 5.04 sec
[bwa_aln_core] print alignments... 0.43 sec
[bwa_aln_core] 5767168 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 32.02 sec
[bwa_aln_core] refine gapped alignments... 4.86 sec
[bwa_aln_core] print alignments... 0.55 sec
[bwa_aln_core] 6029312 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 32.28 sec
[bwa_aln_core] refine gapped alignments... 4.86 sec
[bwa_aln_core] print alignments... 0.56 sec
[bwa_aln_core] 6291456 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 32.39 sec
[bwa_aln_core] refine gapped alignments... 4.88 sec
[bwa_aln_core] print alignments... 0.61 sec
[bwa_aln_core] 6553600 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 33.23 sec
[bwa_aln_core] refine gapped alignments... 4.93 sec
[bwa_aln_core] print alignments... 0.55 sec
[bwa_aln_core] 6815744 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 31.93 sec
[bwa_aln_core] refine gapped alignments... 4.91 sec
[bwa_aln_core] print alignments... 0.51 sec
[bwa_aln_core] 7077888 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 32.64 sec
[bwa_aln_core] refine gapped alignments... 5.08 sec
[bwa_aln_core] print alignments... 0.52 sec
[bwa_aln_core] 7340032 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 33.39 sec
[bwa_aln_core] refine gapped alignments... 4.90 sec
[bwa_aln_core] print alignments... 0.51 sec
[bwa_aln_core] 7602176 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 31.49 sec
[bwa_aln_core] refine gapped alignments... 4.92 sec
[bwa_aln_core] print alignments... 0.55 sec
[bwa_aln_core] 7864320 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 32.32 sec
[bwa_aln_core] refine gapped alignments... 4.94 sec
[bwa_aln_core] print alignments... 0.54 sec
[bwa_aln_core] 8126464 sequences have been processed.
[bwa_read_seq] 0.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 32.46 sec
[bwa_aln_core] refine gapped alignments... 4.96 sec
[bwa_aln_core] print alignments... 0.61 sec
[bwa_aln_core] 8388608 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 33.04 sec
[bwa_aln_core] refine gapped alignments... 5.08 sec
[bwa_aln_core] print alignments... 0.53 sec
[bwa_aln_core] 8650752 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 32.74 sec
[bwa_aln_core] refine gapped alignments... 5.08 sec
[bwa_aln_core] print alignments... 0.59 sec
[bwa_aln_core] 8912896 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 31.81 sec
[bwa_aln_core] refine gapped alignments... 5.14 sec
[bwa_aln_core] print alignments... 0.50 sec
[bwa_aln_core] 9175040 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 31.96 sec
[bwa_aln_core] refine gapped alignments... 5.28 sec
[bwa_aln_core] print alignments... 0.51 sec
[bwa_aln_core] 9437184 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 32.36 sec
[bwa_aln_core] refine gapped alignments... 6.13 sec
[bwa_aln_core] print alignments... 0.58 sec
[bwa_aln_core] 9699328 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 32.48 sec
[bwa_aln_core] refine gapped alignments... 5.16 sec
[bwa_aln_core] print alignments... 0.53 sec
[bwa_aln_core] 9961472 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 31.93 sec
[bwa_aln_core] refine gapped alignments... 5.27 sec
[bwa_aln_core] print alignments... 0.50 sec
[bwa_aln_core] 10223616 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 32.16 sec
[bwa_aln_core] refine gapped alignments... 5.26 sec
[bwa_aln_core] print alignments... 0.59 sec
[bwa_aln_core] 10485760 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 32.50 sec
[bwa_aln_core] refine gapped alignments... 5.14 sec
[bwa_aln_core] print alignments... 0.48 sec
[bwa_aln_core] 10747904 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 31.66 sec
[bwa_aln_core] refine gapped alignments... 5.09 sec
[bwa_aln_core] print alignments... 0.56 sec
[bwa_aln_core] 11010048 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 31.63 sec
[bwa_aln_core] refine gapped alignments... 5.22 sec
[bwa_aln_core] print alignments... 0.59 sec
[bwa_aln_core] 11272192 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 31.70 sec
[bwa_aln_core] refine gapped alignments... 5.15 sec
[bwa_aln_core] print alignments... 0.45 sec
[bwa_aln_core] 11534336 sequences have been processed.
[bwa_read_seq] 0.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 31.90 sec
[bwa_aln_core] refine gapped alignments... 5.28 sec
[bwa_aln_core] print alignments... 0.62 sec
[bwa_aln_core] 11796480 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 32.10 sec
[bwa_aln_core] refine gapped alignments... 5.11 sec
[bwa_aln_core] print alignments... 0.51 sec
[bwa_aln_core] 12058624 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 32.33 sec
[bwa_aln_core] refine gapped alignments... 5.20 sec
[bwa_aln_core] print alignments... 0.56 sec
[bwa_aln_core] 12320768 sequences have been processed.
[bwa_read_seq] 0.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 32.26 sec
[bwa_aln_core] refine gapped alignments... 5.17 sec
[bwa_aln_core] print alignments... 0.53 sec
[bwa_aln_core] 12582912 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 32.20 sec
[bwa_aln_core] refine gapped alignments... 5.19 sec
[bwa_aln_core] print alignments... 0.42 sec
[bwa_aln_core] 12845056 sequences have been processed.
[bwa_read_seq] 0.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 31.98 sec
[bwa_aln_core] refine gapped alignments... 5.10 sec
[bwa_aln_core] print alignments... 0.43 sec
[bwa_aln_core] 13107200 sequences have been processed.
[bwa_read_seq] 0.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 31.92 sec
[bwa_aln_core] refine gapped alignments... 5.14 sec
[bwa_aln_core] print alignments... 0.34 sec
[bwa_aln_core] 13369344 sequences have been processed.
[bwa_read_seq] 0.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 31.74 sec
[bwa_aln_core] refine gapped alignments... 5.81 sec
[bwa_aln_core] print alignments... 0.58 sec
[bwa_aln_core] 13631488 sequences have been processed.
[bwa_read_seq] 0.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 31.61 sec
[bwa_aln_core] refine gapped alignments... 5.12 sec
[bwa_aln_core] print alignments... 0.41 sec
[bwa_aln_core] 13893632 sequences have been processed.
[bwa_read_seq] 0.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 31.65 sec
[bwa_aln_core] refine gapped alignments... 5.14 sec
[bwa_aln_core] print alignments... 0.38 sec
[bwa_aln_core] 14155776 sequences have been processed.
[bwa_read_seq] 0.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 31.63 sec
[bwa_aln_core] refine gapped alignments... 5.20 sec
[bwa_aln_core] print alignments... 0.38 sec
[bwa_aln_core] 14417920 sequences have been processed.
[bwa_read_seq] 0.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 31.97 sec
[bwa_aln_core] refine gapped alignments... 5.52 sec
[bwa_aln_core] print alignments... 0.43 sec
[bwa_aln_core] 14680064 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 31.45 sec
[bwa_aln_core] refine gapped alignments... 5.21 sec
[bwa_aln_core] print alignments... 0.43 sec
[bwa_aln_core] 14942208 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 33.41 sec
[bwa_aln_core] refine gapped alignments... 5.13 sec
[bwa_aln_core] print alignments... 0.45 sec
[bwa_aln_core] 15204352 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 33.90 sec
[bwa_aln_core] refine gapped alignments... 5.14 sec
[bwa_aln_core] print alignments... 0.40 sec
[bwa_aln_core] 15466496 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 32.48 sec
[bwa_aln_core] refine gapped alignments... 5.16 sec
[bwa_aln_core] print alignments... 0.41 sec
[bwa_aln_core] 15728640 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 31.70 sec
[bwa_aln_core] refine gapped alignments... 5.11 sec
[bwa_aln_core] print alignments... 0.33 sec
[bwa_aln_core] 15990784 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 31.48 sec
[bwa_aln_core] refine gapped alignments... 5.11 sec
[bwa_aln_core] print alignments... 0.41 sec
[bwa_aln_core] 16252928 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 31.57 sec
[bwa_aln_core] refine gapped alignments... 5.20 sec
[bwa_aln_core] print alignments... 0.42 sec
[bwa_aln_core] 16515072 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 32.93 sec
[bwa_aln_core] refine gapped alignments... 5.15 sec
[bwa_aln_core] print alignments... 0.33 sec
[bwa_aln_core] 16777216 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 31.50 sec
[bwa_aln_core] refine gapped alignments... 5.15 sec
[bwa_aln_core] print alignments... 0.32 sec
[bwa_aln_core] 17039360 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 31.92 sec
[bwa_aln_core] refine gapped alignments... 5.15 sec
[bwa_aln_core] print alignments... 0.41 sec
[bwa_aln_core] 17301504 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 31.59 sec
[bwa_aln_core] refine gapped alignments... 5.09 sec
[bwa_aln_core] print alignments... 0.32 sec
[bwa_aln_core] 17563648 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 31.79 sec
[bwa_aln_core] refine gapped alignments... 5.13 sec
[bwa_aln_core] print alignments... 0.48 sec
[bwa_aln_core] 17825792 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 31.58 sec
[bwa_aln_core] refine gapped alignments... 4.95 sec
[bwa_aln_core] print alignments... 0.51 sec
[bwa_aln_core] 18087936 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 33.14 sec
[bwa_aln_core] refine gapped alignments... 5.26 sec
[bwa_aln_core] print alignments... 0.34 sec
[bwa_aln_core] 18350080 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 31.73 sec
[bwa_aln_core] refine gapped alignments... 5.01 sec
[bwa_aln_core] print alignments... 0.33 sec
[bwa_aln_core] 18612224 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 32.20 sec
[bwa_aln_core] refine gapped alignments... 5.13 sec
[bwa_aln_core] print alignments... 0.42 sec
[bwa_aln_core] 18874368 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 31.73 sec
[bwa_aln_core] refine gapped alignments... 5.06 sec
[bwa_aln_core] print alignments... 0.41 sec
[bwa_aln_core] 19136512 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 32.48 sec
[bwa_aln_core] refine gapped alignments... 5.14 sec
[bwa_aln_core] print alignments... 0.33 sec
[bwa_aln_core] 19398656 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 31.55 sec
[bwa_aln_core] refine gapped alignments... 5.13 sec
[bwa_aln_core] print alignments... 0.34 sec
[bwa_aln_core] 19660800 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 31.48 sec
[bwa_aln_core] refine gapped alignments... 5.14 sec
[bwa_aln_core] print alignments... 0.32 sec
[bwa_aln_core] 19922944 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 27.88 sec
[bwa_aln_core] refine gapped alignments... 3.03 sec
[bwa_aln_core] print alignments... 0.37 sec
[bwa_aln_core] 20185088 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 33.60 sec
[bwa_aln_core] refine gapped alignments... 3.32 sec
[bwa_aln_core] print alignments... 0.31 sec
[bwa_aln_core] 20447232 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 29.42 sec
[bwa_aln_core] refine gapped alignments... 5.06 sec
[bwa_aln_core] print alignments... 0.31 sec
[bwa_aln_core] 20709376 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 22.90 sec
[bwa_aln_core] refine gapped alignments... 1.26 sec
[bwa_aln_core] print alignments... 0.46 sec
[bwa_aln_core] 20971520 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 31.31 sec
[bwa_aln_core] refine gapped alignments... 3.40 sec
[bwa_aln_core] print alignments... 0.33 sec
[bwa_aln_core] 21233664 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 31.25 sec
[bwa_aln_core] refine gapped alignments... 5.25 sec
[bwa_aln_core] print alignments... 0.36 sec
[bwa_aln_core] 21495808 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 32.00 sec
[bwa_aln_core] refine gapped alignments... 5.18 sec
[bwa_aln_core] print alignments... 0.41 sec
[bwa_aln_core] 21757952 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 34.06 sec
[bwa_aln_core] refine gapped alignments... 4.90 sec
[bwa_aln_core] print alignments... 0.53 sec
[bwa_aln_core] 22020096 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 26.40 sec
[bwa_aln_core] refine gapped alignments... 0.82 sec
[bwa_aln_core] print alignments... 0.47 sec
[bwa_aln_core] 22282240 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 28.56 sec
[bwa_aln_core] refine gapped alignments... 0.36 sec
[bwa_aln_core] print alignments... 0.41 sec
[bwa_aln_core] 22544384 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 28.91 sec
[bwa_aln_core] refine gapped alignments... 0.36 sec
[bwa_aln_core] print alignments... 0.33 sec
[bwa_aln_core] 22806528 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 27.19 sec
[bwa_aln_core] refine gapped alignments... 1.97 sec
[bwa_aln_core] print alignments... 0.34 sec
[bwa_aln_core] 23068672 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 29.33 sec
[bwa_aln_core] refine gapped alignments... 0.37 sec
[bwa_aln_core] print alignments... 0.33 sec
[bwa_aln_core] 23330816 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 28.87 sec
[bwa_aln_core] refine gapped alignments... 0.61 sec
[bwa_aln_core] print alignments... 0.45 sec
[bwa_aln_core] 23592960 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 29.00 sec
[bwa_aln_core] refine gapped alignments... 1.00 sec
[bwa_aln_core] print alignments... 0.32 sec
[bwa_aln_core] 23855104 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 27.38 sec
[bwa_aln_core] refine gapped alignments... 0.99 sec
[bwa_aln_core] print alignments... 0.33 sec
[bwa_aln_core] 24117248 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 27.31 sec
[bwa_aln_core] refine gapped alignments... 0.99 sec
[bwa_aln_core] print alignments... 0.47 sec
[bwa_aln_core] 24379392 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 27.80 sec
[bwa_aln_core] refine gapped alignments... 1.06 sec
[bwa_aln_core] print alignments... 0.41 sec
[bwa_aln_core] 24641536 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 27.62 sec
[bwa_aln_core] refine gapped alignments... 0.97 sec
[bwa_aln_core] print alignments... 0.33 sec
[bwa_aln_core] 24903680 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 27.49 sec
[bwa_aln_core] refine gapped alignments... 2.84 sec
[bwa_aln_core] print alignments... 0.39 sec
[bwa_aln_core] 25165824 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 26.98 sec
[bwa_aln_core] refine gapped alignments... 0.42 sec
[bwa_aln_core] print alignments... 0.39 sec
[bwa_aln_core] 25427968 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 28.18 sec
[bwa_aln_core] refine gapped alignments... 1.16 sec
[bwa_aln_core] print alignments... 0.38 sec
[bwa_aln_core] 25690112 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 28.48 sec
[bwa_aln_core] refine gapped alignments... 1.19 sec
[bwa_aln_core] print alignments... 0.35 sec
[bwa_aln_core] 25952256 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 27.45 sec
[bwa_aln_core] refine gapped alignments... 0.60 sec
[bwa_aln_core] print alignments... 0.40 sec
[bwa_aln_core] 26214400 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 27.28 sec
[bwa_aln_core] refine gapped alignments... 0.61 sec
[bwa_aln_core] print alignments... 0.46 sec
[bwa_aln_core] 26476544 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 27.76 sec
[bwa_aln_core] refine gapped alignments... 0.72 sec
[bwa_aln_core] print alignments... 0.45 sec
[bwa_aln_core] 26738688 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 27.81 sec
[bwa_aln_core] refine gapped alignments... 1.03 sec
[bwa_aln_core] print alignments... 0.41 sec
[bwa_aln_core] 27000832 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 28.01 sec
[bwa_aln_core] refine gapped alignments... 1.10 sec
[bwa_aln_core] print alignments... 0.33 sec
[bwa_aln_core] 27262976 sequences have been processed.
[bwa_read_seq] 1.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 25.60 sec
[bwa_aln_core] refine gapped alignments... 0.71 sec
[bwa_aln_core] print alignments... 0.01 sec
[bwa_aln_core] 27277223 sequences have been processed.
[main] Version: 0.7.13-r1126
[main] CMD: bwa samse /mnt/data/bds_pipeline_genome_data/hg38/bwa_index/GRCh38.p3.genome.fa /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H4ac/out/align/rep1/SRR1015998.sai /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/RawReadsFiles/SRR1015998.fastq.gz
[main] Real time: 3830.019 sec; CPU: 3764.296 sec

 
 		 

    
  
 
  Num   5  
 
  ID   task.postalign_bam.dedup_bam_1_ctl1.line_95.id_14  
 
  Name   dedup_bam_1 ctl1 
 
  Thread   thread_42  
 
  PID   35952  
 
 		  
 
  OK   true   
 
  Exit Code   0   
 
  Retries    
 
  State   FINISHED  
 
  Dep.   OK  
 
  Cpus    2 
 
  Mem    
 
 		  
 
  Start   2017-01-29 00:07:11  
 
  End   2017-01-29 00:09:10  
 
  Elapsed   00:01:58  
 
  Timeout  00:00:-1 
 
  Wall Timeout   100 days 
 
 		  
 
  Input files  /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H4ac/out/align/ctl1/ENCFF001HNC.bam
   
 
  Output files   /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H4ac/out/align/ctl1/ENCFF001HNC.filt.bam
  
 
  Dependencies     
 
 		  
 
# SYS command. line 97

 if [[ -f $(which conda) && $(conda env list | grep aquas_chipseq | wc -l) != "0" ]]; then source activate aquas_chipseq; sleep 5; fi;  export PATH=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/.:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/modules:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/utils:${PATH}:/bin:/usr/bin:/usr/local/bin:${HOME}/.bds; set -o pipefail; STARTTIME=$(date +%s); renice -n 10 $$

# SYS command. line 105

 if [[ 0 > 0 ]]; then \
				sambamba sort -t 2 /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H4ac/out/align/ctl1/ENCFF001HNC.bam -n -o /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H4ac/out/align/ctl1/ENCFF001HNC.qnmsrt.bam; \
				samtools view -h /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H4ac/out/align/ctl1/ENCFF001HNC.qnmsrt.bam | $(which assign_multimappers.py) -k 0 | \
				samtools view -F 1804 -Su /dev/stdin | \
				sambamba sort -t 2 /dev/stdin -o /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H4ac/out/align/ctl1/ENCFF001HNC.filt.bam; \
				rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H4ac/out/align/ctl1/ENCFF001HNC.qnmsrt.bam; \
			    else \
			    	samtools view -F 1804 -q 30 -u /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H4ac/out/align/ctl1/ENCFF001HNC.bam | \
			    	sambamba sort -t 2 /dev/stdin -o /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H4ac/out/align/ctl1/ENCFF001HNC.filt.bam; \
			    fi

# SYS command. line 116

 TASKTIME=$[$(date +%s)-${STARTTIME}]; if [ ${TASKTIME} -lt 60 ]; then echo "Waiting for $[60-${TASKTIME}] seconds."; sleep $[60-${TASKTIME}]; fi
 
 
   
--------------------Stdout--------------------
21129 (process ID) old priority 0, new priority 10

  
 		 

    
  
 
  Num   6  
 
  ID   task.postalign_bam.markdup_bam_picard_ctl1.line_348.id_15  
 
  Name   markdup_bam_picard ctl1 
 
  Thread   thread_42  
 
  PID   35953  
 
 		  
 
  OK   true   
 
  Exit Code   0   
 
  Retries    
 
  State   FINISHED  
 
  Dep.   OK  
 
  Cpus    1 
 
  Mem    
 
 		  
 
  Start   2017-01-29 00:09:11  
 
  End   2017-01-29 00:12:06  
 
  Elapsed   00:02:55  
 
  Timeout  00:00:-1 
 
  Wall Timeout   100 days 
 
 		  
 
  Input files  /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H4ac/out/align/ctl1/ENCFF001HNC.filt.bam
   
 
  Output files   /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H4ac/out/align/ctl1/ENCFF001HNC.dupmark.bam
/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H4ac/out/qc/ctl1/ENCFF001HNC.dup.qc
  
 
  Dependencies     
 
 		  
 
# SYS command. line 350

 if [[ -f $(which conda) && $(conda env list | grep aquas_chipseq | wc -l) != "0" ]]; then source activate aquas_chipseq; sleep 5; fi;  export PATH=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/.:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/modules:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/utils:${PATH}:/bin:/usr/bin:/usr/local/bin:${HOME}/.bds; set -o pipefail; STARTTIME=$(date +%s); renice -n 10 $$

# SYS command. line 354

 export _JAVA_OPTIONS="-Xms256M -Xmx12G -XX:ParallelGCThreads=1"

# SYS command. line 360

 if [ -f "${PICARDROOT}/picard.jar" ]; then \
		      MARKDUP="${PICARDROOT}/picard.jar MarkDuplicates"; \
		    elif [ -f "${PICARDROOT}/MarkDuplicates.jar" ]; then \
		      MARKDUP="${PICARDROOT}/MarkDuplicates.jar"; \
		    elif [ $(which picard 2> /dev/null | wc -l || echo) == "1" ]; then \
		      MARKDUP="$(ls $(dirname $(which picard))/../share/picard*/MarkDuplicates.jar 2> /dev/null || echo)"; \
		    fi

# SYS command. line 369

 if [ -f "${MARKDUP}" ]; then \
			java -Xmx4G -jar ${MARKDUP} \
				INPUT="/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H4ac/out/align/ctl1/ENCFF001HNC.filt.bam" OUTPUT="/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H4ac/out/align/ctl1/ENCFF001HNC.dupmark.bam" \
				METRICS_FILE="/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H4ac/out/qc/ctl1/ENCFF001HNC.dup.qc" VALIDATION_STRINGENCY=LENIENT \
				ASSUME_SORTED=true REMOVE_DUPLICATES=false; \
		    else \
			picard MarkDuplicates \
				INPUT="/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H4ac/out/align/ctl1/ENCFF001HNC.filt.bam" OUTPUT="/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H4ac/out/align/ctl1/ENCFF001HNC.dupmark.bam" \
				METRICS_FILE="/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H4ac/out/qc/ctl1/ENCFF001HNC.dup.qc" VALIDATION_STRINGENCY=LENIENT \
				ASSUME_SORTED=true REMOVE_DUPLICATES=false; \
			fi

# SYS command. line 381

 TASKTIME=$[$(date +%s)-${STARTTIME}]; if [ ${TASKTIME} -lt 60 ]; then echo "Waiting for $[60-${TASKTIME}] seconds."; sleep $[60-${TASKTIME}]; fi
 
 
   
--------------------Stdout--------------------
6336 (process ID) old priority 0, new priority 10

 
--------------------Stderr--------------------
Picked up _JAVA_OPTIONS: -Xms256M -Xmx12G -XX:ParallelGCThreads=1
[Sun Jan 29 00:09:21 PST 2017] picard.sam.markduplicates.MarkDuplicates INPUT=[/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H4ac/out/align/ctl1/ENCFF001HNC.filt.bam] OUTPUT=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H4ac/out/align/ctl1/ENCFF001HNC.dupmark.bam METRICS_FILE=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H4ac/out/qc/ctl1/ENCFF001HNC.dup.qc REMOVE_DUPLICATES=false ASSUME_SORTED=true VALIDATION_STRINGENCY=LENIENT    MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates DUPLICATE_SCORING_STRATEGY=SUM_OF_BASE_QUALITIES READ_NAME_REGEX=[a-zA-Z0-9]+:[0-9]:([0-9]+):([0-9]+):([0-9]+).* OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 VERBOSITY=INFO QUIET=false COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false
[Sun Jan 29 00:09:21 PST 2017] Executing as imk1@kadru on Linux 4.4.0-22-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_92-b15; Picard version: 1.126(4691ee611ac205d4afe2a1b7a2ea975a6f997426_1417447214) IntelDeflater
INFO	2017-01-29 00:09:21	MarkDuplicates	Start of doWork freeMemory: 254879616; totalMemory: 257425408; maxMemory: 11453595648
INFO	2017-01-29 00:09:21	MarkDuplicates	Reading input file and constructing read end information.
INFO	2017-01-29 00:09:21	MarkDuplicates	Will retain up to 44052290 data points before spilling to disk.
INFO	2017-01-29 00:09:31	MarkDuplicates	Read     1,000,000 records.  Elapsed time: 00:00:06s.  Time for last 1,000,000:    6s.  Last read position: chr2:7,720,599
INFO	2017-01-29 00:09:31	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2017-01-29 00:09:36	MarkDuplicates	Read     2,000,000 records.  Elapsed time: 00:00:12s.  Time for last 1,000,000:    5s.  Last read position: chr3:32,290,878
INFO	2017-01-29 00:09:36	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2017-01-29 00:09:41	MarkDuplicates	Read     3,000,000 records.  Elapsed time: 00:00:17s.  Time for last 1,000,000:    5s.  Last read position: chr5:31,410,244
INFO	2017-01-29 00:09:41	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2017-01-29 00:09:44	MarkDuplicates	Read     4,000,000 records.  Elapsed time: 00:00:20s.  Time for last 1,000,000:    3s.  Last read position: chr6:76,055,404
INFO	2017-01-29 00:09:44	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2017-01-29 00:09:51	MarkDuplicates	Read     5,000,000 records.  Elapsed time: 00:00:27s.  Time for last 1,000,000:    7s.  Last read position: chr7:134,138,515
INFO	2017-01-29 00:09:51	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2017-01-29 00:09:54	MarkDuplicates	Read     6,000,000 records.  Elapsed time: 00:00:30s.  Time for last 1,000,000:    2s.  Last read position: chr9:137,609,223
INFO	2017-01-29 00:09:54	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2017-01-29 00:10:00	MarkDuplicates	Read     7,000,000 records.  Elapsed time: 00:00:36s.  Time for last 1,000,000:    5s.  Last read position: chr11:121,062,334
INFO	2017-01-29 00:10:00	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2017-01-29 00:10:07	MarkDuplicates	Read     8,000,000 records.  Elapsed time: 00:00:43s.  Time for last 1,000,000:    7s.  Last read position: chr14:86,188,790
INFO	2017-01-29 00:10:07	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2017-01-29 00:10:10	MarkDuplicates	Read     9,000,000 records.  Elapsed time: 00:00:45s.  Time for last 1,000,000:    2s.  Last read position: chr17:58,813,264
INFO	2017-01-29 00:10:10	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2017-01-29 00:10:14	MarkDuplicates	Read    10,000,000 records.  Elapsed time: 00:00:50s.  Time for last 1,000,000:    4s.  Last read position: chr20:35,666,706
INFO	2017-01-29 00:10:14	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2017-01-29 00:10:17	MarkDuplicates	Read    11,000,000 records.  Elapsed time: 00:00:52s.  Time for last 1,000,000:    2s.  Last read position: chrX:100,440,272
INFO	2017-01-29 00:10:17	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2017-01-29 00:10:19	MarkDuplicates	Read 11369002 records. 0 pairs never matched.
INFO	2017-01-29 00:10:22	MarkDuplicates	After buildSortedReadEndLists freeMemory: 3577133880; totalMemory: 4728029184; maxMemory: 11453595648
INFO	2017-01-29 00:10:22	MarkDuplicates	Will retain up to 357924864 duplicate indices before spilling to disk.
INFO	2017-01-29 00:10:22	MarkDuplicates	Traversing read pair information and detecting duplicates.
INFO	2017-01-29 00:10:22	MarkDuplicates	Traversing fragment information and detecting duplicates.
INFO	2017-01-29 00:10:23	MarkDuplicates	Sorting list of duplicate records.
INFO	2017-01-29 00:10:24	MarkDuplicates	After generateDuplicateIndexes freeMemory: 1794759504; totalMemory: 4728029184; maxMemory: 11453595648
INFO	2017-01-29 00:10:24	MarkDuplicates	Marking 167589 records as duplicates.
INFO	2017-01-29 00:10:24	MarkDuplicates	Found 0 optical duplicate clusters.
INFO	2017-01-29 00:11:53	MarkDuplicates	Written    10,000,000 records.  Elapsed time: 00:01:29s.  Time for last 10,000,000:   89s.  Last read position: chr20:35,666,706
INFO	2017-01-29 00:12:04	MarkDuplicates	Before output close freeMemory: 8185461120; totalMemory: 8264876032; maxMemory: 11453595648
INFO	2017-01-29 00:12:05	MarkDuplicates	After output close freeMemory: 8293987576; totalMemory: 8373403648; maxMemory: 11453595648
[Sun Jan 29 00:12:05 PST 2017] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 2.73 minutes.
Runtime.totalMemory()=8373403648

 
 		 

    
  
 
  Num   7  
 
  ID   task.postalign_bam.dedup_bam_2_ctl1.line_144.id_16  
 
  Name   dedup_bam_2 ctl1 
 
  Thread   thread_42  
 
  PID   35958  
 
 		  
 
  OK   true   
 
  Exit Code   0   
 
  Retries    
 
  State   FINISHED  
 
  Dep.   OK  
 
  Cpus    2 
 
  Mem    
 
 		  
 
  Start   2017-01-29 00:12:08  
 
  End   2017-01-29 00:17:35  
 
  Elapsed   00:05:27  
 
  Timeout  00:00:-1 
 
  Wall Timeout   100 days 
 
 		  
 
  Input files  /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H4ac/out/align/ctl1/ENCFF001HNC.dupmark.bam
   
 
  Output files   /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H4ac/out/align/ctl1/ENCFF001HNC.nodup.bam
/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H4ac/out/qc/ctl1/ENCFF001HNC.nodup.flagstat.qc
/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H4ac/out/qc/ctl1/ENCFF001HNC.nodup.pbc.qc
  
 
  Dependencies     
 
 		  
 
# SYS command. line 146

 if [[ -f $(which conda) && $(conda env list | grep aquas_chipseq | wc -l) != "0" ]]; then source activate aquas_chipseq; sleep 5; fi;  export PATH=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/.:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/modules:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/utils:${PATH}:/bin:/usr/bin:/usr/local/bin:${HOME}/.bds; set -o pipefail; STARTTIME=$(date +%s); renice -n 10 $$

# SYS command. line 150

 samtools view -F 1804 -b /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H4ac/out/align/ctl1/ENCFF001HNC.dupmark.bam > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H4ac/out/align/ctl1/ENCFF001HNC.nodup.bam

# SYS command. line 153

 sambamba index -t 2 /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H4ac/out/align/ctl1/ENCFF001HNC.nodup.bam

# SYS command. line 155

 sambamba flagstat -t 2 /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H4ac/out/align/ctl1/ENCFF001HNC.nodup.bam > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H4ac/out/qc/ctl1/ENCFF001HNC.nodup.flagstat.qc

# SYS command. line 165

 bedtools bamtobed -i /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H4ac/out/align/ctl1/ENCFF001HNC.dupmark.bam | \
				awk 'BEGIN{OFS="\t"}{print $1,$2,$3,$6}' | \
				grep -v 'chrM' | sort | uniq -c | \
				awk 'BEGIN{mt=0;m0=0;m1=0;m2=0} ($1==1){m1=m1+1} ($1==2){m2=m2+1} {m0=m0+1} {mt=mt+$1} END{m1_m2=-1.0; if(m2>0) m1_m2=m1/m2; printf "%d\t%d\t%d\t%d\t%f\t%f\t%f\n",mt,m0,m1,m2,m0/mt,m1/m0,m1_m2}' > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H4ac/out/qc/ctl1/ENCFF001HNC.nodup.pbc.qc

# SYS command. line 169

 TASKTIME=$[$(date +%s)-${STARTTIME}]; if [ ${TASKTIME} -lt 60 ]; then echo "Waiting for $[60-${TASKTIME}] seconds."; sleep $[60-${TASKTIME}]; fi
 
 
   
--------------------Stdout--------------------
60335 (process ID) old priority 0, new priority 10

  
 		 

    
  
 
  Num   8  
 
  ID   task.postalign_bam.bam_to_tag_ctl1.line_505.id_17  
 
  Name   bam_to_tag ctl1 
 
  Thread   thread_42  
 
  PID   35968  
 
 		  
 
  OK   true   
 
  Exit Code   0   
 
  Retries    
 
  State   FINISHED  
 
  Dep.   OK  
 
  Cpus     
 
  Mem    
 
 		  
 
  Start   2017-01-29 00:17:37  
 
  End   2017-01-29 00:18:53  
 
  Elapsed   00:01:15  
 
  Timeout  00:00:-1 
 
  Wall Timeout   100 days 
 
 		  
 
  Input files  /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H4ac/out/align/ctl1/ENCFF001HNC.nodup.bam
   
 
  Output files   /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H4ac/out/align/ctl1/ENCFF001HNC.nodup.tagAlign.gz
  
 
  Dependencies     
 
 		  
 
# SYS command. line 507

 if [[ -f $(which conda) && $(conda env list | grep aquas_chipseq | wc -l) != "0" ]]; then source activate aquas_chipseq; sleep 5; fi;  export PATH=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/.:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/modules:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/utils:${PATH}:/bin:/usr/bin:/usr/local/bin:${HOME}/.bds; set -o pipefail; STARTTIME=$(date +%s); renice -n 10 $$

# SYS command. line 510

 bedtools bamtobed -i /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H4ac/out/align/ctl1/ENCFF001HNC.nodup.bam | awk 'BEGIN{OFS="\t"}{$4="N";$5="1000";print $0}' | gzip -nc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H4ac/out/align/ctl1/ENCFF001HNC.nodup.tagAlign.gz

# SYS command. line 512

 echo

# SYS command. line 514

 TASKTIME=$[$(date +%s)-${STARTTIME}]; if [ ${TASKTIME} -lt 60 ]; then echo "Waiting for $[60-${TASKTIME}] seconds."; sleep $[60-${TASKTIME}]; fi
 
 
   
--------------------Stdout--------------------
6880 (process ID) old priority 0, new priority 10

Waiting for 33 seconds.

  
 		 

    
  
 
  Num   9  
 
  ID   task.postalign_bam.dedup_bam_1_rep1.line_95.id_18  
 
  Name   dedup_bam_1 rep1 
 
  Thread   thread_41  
 
  PID   35999  
 
 		  
 
  OK   true   
 
  Exit Code   0   
 
  Retries    
 
  State   FINISHED  
 
  Dep.   OK  
 
  Cpus    2 
 
  Mem    
 
 		  
 
  Start   2017-01-29 00:38:40  
 
  End   2017-01-29 00:41:01  
 
  Elapsed   00:02:21  
 
  Timeout  00:00:-1 
 
  Wall Timeout   100 days 
 
 		  
 
  Input files  /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H4ac/out/align/rep1/SRR1015998.bam
   
 
  Output files   /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H4ac/out/align/rep1/SRR1015998.filt.bam
  
 
  Dependencies     
 
 		  
 
# SYS command. line 97

 if [[ -f $(which conda) && $(conda env list | grep aquas_chipseq | wc -l) != "0" ]]; then source activate aquas_chipseq; sleep 5; fi;  export PATH=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/.:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/modules:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/utils:${PATH}:/bin:/usr/bin:/usr/local/bin:${HOME}/.bds; set -o pipefail; STARTTIME=$(date +%s); renice -n 10 $$

# SYS command. line 105

 if [[ 0 > 0 ]]; then \
				sambamba sort -t 2 /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H4ac/out/align/rep1/SRR1015998.bam -n -o /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H4ac/out/align/rep1/SRR1015998.qnmsrt.bam; \
				samtools view -h /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H4ac/out/align/rep1/SRR1015998.qnmsrt.bam | $(which assign_multimappers.py) -k 0 | \
				samtools view -F 1804 -Su /dev/stdin | \
				sambamba sort -t 2 /dev/stdin -o /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H4ac/out/align/rep1/SRR1015998.filt.bam; \
				rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H4ac/out/align/rep1/SRR1015998.qnmsrt.bam; \
			    else \
			    	samtools view -F 1804 -q 30 -u /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H4ac/out/align/rep1/SRR1015998.bam | \
			    	sambamba sort -t 2 /dev/stdin -o /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H4ac/out/align/rep1/SRR1015998.filt.bam; \
			    fi

# SYS command. line 116

 TASKTIME=$[$(date +%s)-${STARTTIME}]; if [ ${TASKTIME} -lt 60 ]; then echo "Waiting for $[60-${TASKTIME}] seconds."; sleep $[60-${TASKTIME}]; fi
 
 
   
--------------------Stdout--------------------
17849 (process ID) old priority 0, new priority 10

  
 		 

    
  
 
  Num   10  
 
  ID   task.postalign_bam.markdup_bam_picard_rep1.line_348.id_19  
 
  Name   markdup_bam_picard rep1 
 
  Thread   thread_41  
 
  PID   36003  
 
 		  
 
  OK   true   
 
  Exit Code   0   
 
  Retries    
 
  State   FINISHED  
 
  Dep.   OK  
 
  Cpus    1 
 
  Mem    
 
 		  
 
  Start   2017-01-29 00:41:03  
 
  End   2017-01-29 00:44:55  
 
  Elapsed   00:03:51  
 
  Timeout  00:00:-1 
 
  Wall Timeout   100 days 
 
 		  
 
  Input files  /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H4ac/out/align/rep1/SRR1015998.filt.bam
   
 
  Output files   /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H4ac/out/align/rep1/SRR1015998.dupmark.bam
/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H4ac/out/qc/rep1/SRR1015998.dup.qc
  
 
  Dependencies     
 
 		  
 
# SYS command. line 350

 if [[ -f $(which conda) && $(conda env list | grep aquas_chipseq | wc -l) != "0" ]]; then source activate aquas_chipseq; sleep 5; fi;  export PATH=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/.:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/modules:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/utils:${PATH}:/bin:/usr/bin:/usr/local/bin:${HOME}/.bds; set -o pipefail; STARTTIME=$(date +%s); renice -n 10 $$

# SYS command. line 354

 export _JAVA_OPTIONS="-Xms256M -Xmx12G -XX:ParallelGCThreads=1"

# SYS command. line 360

 if [ -f "${PICARDROOT}/picard.jar" ]; then \
		      MARKDUP="${PICARDROOT}/picard.jar MarkDuplicates"; \
		    elif [ -f "${PICARDROOT}/MarkDuplicates.jar" ]; then \
		      MARKDUP="${PICARDROOT}/MarkDuplicates.jar"; \
		    elif [ $(which picard 2> /dev/null | wc -l || echo) == "1" ]; then \
		      MARKDUP="$(ls $(dirname $(which picard))/../share/picard*/MarkDuplicates.jar 2> /dev/null || echo)"; \
		    fi

# SYS command. line 369

 if [ -f "${MARKDUP}" ]; then \
			java -Xmx4G -jar ${MARKDUP} \
				INPUT="/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H4ac/out/align/rep1/SRR1015998.filt.bam" OUTPUT="/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H4ac/out/align/rep1/SRR1015998.dupmark.bam" \
				METRICS_FILE="/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H4ac/out/qc/rep1/SRR1015998.dup.qc" VALIDATION_STRINGENCY=LENIENT \
				ASSUME_SORTED=true REMOVE_DUPLICATES=false; \
		    else \
			picard MarkDuplicates \
				INPUT="/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H4ac/out/align/rep1/SRR1015998.filt.bam" OUTPUT="/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H4ac/out/align/rep1/SRR1015998.dupmark.bam" \
				METRICS_FILE="/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H4ac/out/qc/rep1/SRR1015998.dup.qc" VALIDATION_STRINGENCY=LENIENT \
				ASSUME_SORTED=true REMOVE_DUPLICATES=false; \
			fi

# SYS command. line 381

 TASKTIME=$[$(date +%s)-${STARTTIME}]; if [ ${TASKTIME} -lt 60 ]; then echo "Waiting for $[60-${TASKTIME}] seconds."; sleep $[60-${TASKTIME}]; fi
 
 
   
--------------------Stdout--------------------
8290 (process ID) old priority 0, new priority 10

 
--------------------Stderr--------------------
Picked up _JAVA_OPTIONS: -Xms256M -Xmx12G -XX:ParallelGCThreads=1
[Sun Jan 29 00:41:21 PST 2017] picard.sam.markduplicates.MarkDuplicates INPUT=[/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H4ac/out/align/rep1/SRR1015998.filt.bam] OUTPUT=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H4ac/out/align/rep1/SRR1015998.dupmark.bam METRICS_FILE=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H4ac/out/qc/rep1/SRR1015998.dup.qc REMOVE_DUPLICATES=false ASSUME_SORTED=true VALIDATION_STRINGENCY=LENIENT    MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates DUPLICATE_SCORING_STRATEGY=SUM_OF_BASE_QUALITIES READ_NAME_REGEX=[a-zA-Z0-9]+:[0-9]:([0-9]+):([0-9]+):([0-9]+).* OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 VERBOSITY=INFO QUIET=false COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false
[Sun Jan 29 00:41:21 PST 2017] Executing as imk1@kadru on Linux 4.4.0-22-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_92-b15; Picard version: 1.126(4691ee611ac205d4afe2a1b7a2ea975a6f997426_1417447214) IntelDeflater
INFO	2017-01-29 00:41:22	MarkDuplicates	Start of doWork freeMemory: 254879640; totalMemory: 257425408; maxMemory: 11453595648
INFO	2017-01-29 00:41:22	MarkDuplicates	Reading input file and constructing read end information.
INFO	2017-01-29 00:41:22	MarkDuplicates	Will retain up to 44052290 data points before spilling to disk.
WARNING	2017-01-29 00:41:24	AbstractOpticalDuplicateFinderCommandLineProgram	Default READ_NAME_REGEX '[a-zA-Z0-9]+:[0-9]:([0-9]+):([0-9]+):([0-9]+).*' did not match read name 'SRR1015998.25801790'.  You may need to specify a READ_NAME_REGEX in order to correctly identify optical duplicates.  Note that this message will not be emitted again even if other read names do not match the regex.
INFO	2017-01-29 00:41:30	MarkDuplicates	Read     1,000,000 records.  Elapsed time: 00:00:06s.  Time for last 1,000,000:    6s.  Last read position: chr1:158,547,957
INFO	2017-01-29 00:41:30	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2017-01-29 00:41:33	MarkDuplicates	Read     2,000,000 records.  Elapsed time: 00:00:09s.  Time for last 1,000,000:    3s.  Last read position: chr2:54,963,718
INFO	2017-01-29 00:41:33	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2017-01-29 00:41:38	MarkDuplicates	Read     3,000,000 records.  Elapsed time: 00:00:14s.  Time for last 1,000,000:    4s.  Last read position: chr3:5,390,936
INFO	2017-01-29 00:41:38	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2017-01-29 00:41:43	MarkDuplicates	Read     4,000,000 records.  Elapsed time: 00:00:19s.  Time for last 1,000,000:    5s.  Last read position: chr3:187,779,361
INFO	2017-01-29 00:41:43	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2017-01-29 00:41:46	MarkDuplicates	Read     5,000,000 records.  Elapsed time: 00:00:21s.  Time for last 1,000,000:    2s.  Last read position: chr5:45,083,380
INFO	2017-01-29 00:41:46	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2017-01-29 00:41:52	MarkDuplicates	Read     6,000,000 records.  Elapsed time: 00:00:28s.  Time for last 1,000,000:    6s.  Last read position: chr6:7,878,084
INFO	2017-01-29 00:41:52	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2017-01-29 00:41:56	MarkDuplicates	Read     7,000,000 records.  Elapsed time: 00:00:32s.  Time for last 1,000,000:    4s.  Last read position: chr6:166,558,376
INFO	2017-01-29 00:41:56	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2017-01-29 00:42:01	MarkDuplicates	Read     8,000,000 records.  Elapsed time: 00:00:37s.  Time for last 1,000,000:    4s.  Last read position: chr8:38,310,730
INFO	2017-01-29 00:42:01	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2017-01-29 00:42:04	MarkDuplicates	Read     9,000,000 records.  Elapsed time: 00:00:39s.  Time for last 1,000,000:    2s.  Last read position: chr10:4,919,604
INFO	2017-01-29 00:42:04	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2017-01-29 00:42:10	MarkDuplicates	Read    10,000,000 records.  Elapsed time: 00:00:45s.  Time for last 1,000,000:    6s.  Last read position: chr11:44,968,132
INFO	2017-01-29 00:42:10	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2017-01-29 00:42:16	MarkDuplicates	Read    11,000,000 records.  Elapsed time: 00:00:51s.  Time for last 1,000,000:    6s.  Last read position: chr12:93,266,204
INFO	2017-01-29 00:42:16	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2017-01-29 00:42:18	MarkDuplicates	Read    12,000,000 records.  Elapsed time: 00:00:54s.  Time for last 1,000,000:    2s.  Last read position: chr14:65,838,122
INFO	2017-01-29 00:42:18	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2017-01-29 00:42:22	MarkDuplicates	Read    13,000,000 records.  Elapsed time: 00:00:58s.  Time for last 1,000,000:    4s.  Last read position: chr16:49,335,913
INFO	2017-01-29 00:42:22	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2017-01-29 00:42:25	MarkDuplicates	Read    14,000,000 records.  Elapsed time: 00:01:00s.  Time for last 1,000,000:    2s.  Last read position: chr18:47,791,503
INFO	2017-01-29 00:42:25	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2017-01-29 00:42:36	MarkDuplicates	Read    15,000,000 records.  Elapsed time: 00:01:11s.  Time for last 1,000,000:   10s.  Last read position: chr21:35,918,753
INFO	2017-01-29 00:42:36	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2017-01-29 00:42:38	MarkDuplicates	Read    16,000,000 records.  Elapsed time: 00:01:13s.  Time for last 1,000,000:    2s.  Last read position: chrX:150,522,854
INFO	2017-01-29 00:42:38	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2017-01-29 00:42:38	MarkDuplicates	Read 16106813 records. 0 pairs never matched.
INFO	2017-01-29 00:42:42	MarkDuplicates	After buildSortedReadEndLists freeMemory: 3995644968; totalMemory: 5454168064; maxMemory: 11453595648
INFO	2017-01-29 00:42:42	MarkDuplicates	Will retain up to 357924864 duplicate indices before spilling to disk.
INFO	2017-01-29 00:42:43	MarkDuplicates	Traversing read pair information and detecting duplicates.
INFO	2017-01-29 00:42:43	MarkDuplicates	Traversing fragment information and detecting duplicates.
INFO	2017-01-29 00:42:44	MarkDuplicates	Sorting list of duplicate records.
INFO	2017-01-29 00:43:05	MarkDuplicates	After generateDuplicateIndexes freeMemory: 5268719768; totalMemory: 8206680064; maxMemory: 11453595648
INFO	2017-01-29 00:43:05	MarkDuplicates	Marking 371675 records as duplicates.
INFO	2017-01-29 00:43:05	MarkDuplicates	Found 0 optical duplicate clusters.
INFO	2017-01-29 00:44:12	MarkDuplicates	Written    10,000,000 records.  Elapsed time: 00:01:07s.  Time for last 10,000,000:   67s.  Last read position: chr11:44,968,132
INFO	2017-01-29 00:44:52	MarkDuplicates	Before output close freeMemory: 8544514744; totalMemory: 8625586176; maxMemory: 11453595648
INFO	2017-01-29 00:44:53	MarkDuplicates	After output close freeMemory: 8410295856; totalMemory: 8491368448; maxMemory: 11453595648
[Sun Jan 29 00:44:53 PST 2017] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 3.53 minutes.
Runtime.totalMemory()=8491368448

 
 		 

    
  
 
  Num   11  
 
  ID   task.postalign_bam.dedup_bam_2_rep1.line_144.id_20  
 
  Name   dedup_bam_2 rep1 
 
  Thread   thread_41  
 
  PID   36010  
 
 		  
 
  OK   true   
 
  Exit Code   0   
 
  Retries    
 
  State   FINISHED  
 
  Dep.   OK  
 
  Cpus    2 
 
  Mem    
 
 		  
 
  Start   2017-01-29 00:44:56  
 
  End   2017-01-29 00:48:20  
 
  Elapsed   00:03:24  
 
  Timeout  00:00:-1 
 
  Wall Timeout   100 days 
 
 		  
 
  Input files  /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H4ac/out/align/rep1/SRR1015998.dupmark.bam
   
 
  Output files   /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H4ac/out/align/rep1/SRR1015998.nodup.bam
/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H4ac/out/qc/rep1/SRR1015998.nodup.flagstat.qc
/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H4ac/out/qc/rep1/SRR1015998.nodup.pbc.qc
  
 
  Dependencies     
 
 		  
 
# SYS command. line 146

 if [[ -f $(which conda) && $(conda env list | grep aquas_chipseq | wc -l) != "0" ]]; then source activate aquas_chipseq; sleep 5; fi;  export PATH=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/.:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/modules:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/utils:${PATH}:/bin:/usr/bin:/usr/local/bin:${HOME}/.bds; set -o pipefail; STARTTIME=$(date +%s); renice -n 10 $$

# SYS command. line 150

 samtools view -F 1804 -b /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H4ac/out/align/rep1/SRR1015998.dupmark.bam > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H4ac/out/align/rep1/SRR1015998.nodup.bam

# SYS command. line 153

 sambamba index -t 2 /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H4ac/out/align/rep1/SRR1015998.nodup.bam

# SYS command. line 155

 sambamba flagstat -t 2 /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H4ac/out/align/rep1/SRR1015998.nodup.bam > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H4ac/out/qc/rep1/SRR1015998.nodup.flagstat.qc

# SYS command. line 165

 bedtools bamtobed -i /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H4ac/out/align/rep1/SRR1015998.dupmark.bam | \
				awk 'BEGIN{OFS="\t"}{print $1,$2,$3,$6}' | \
				grep -v 'chrM' | sort | uniq -c | \
				awk 'BEGIN{mt=0;m0=0;m1=0;m2=0} ($1==1){m1=m1+1} ($1==2){m2=m2+1} {m0=m0+1} {mt=mt+$1} END{m1_m2=-1.0; if(m2>0) m1_m2=m1/m2; printf "%d\t%d\t%d\t%d\t%f\t%f\t%f\n",mt,m0,m1,m2,m0/mt,m1/m0,m1_m2}' > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H4ac/out/qc/rep1/SRR1015998.nodup.pbc.qc

# SYS command. line 169

 TASKTIME=$[$(date +%s)-${STARTTIME}]; if [ ${TASKTIME} -lt 60 ]; then echo "Waiting for $[60-${TASKTIME}] seconds."; sleep $[60-${TASKTIME}]; fi
 
 
   
--------------------Stdout--------------------
40289 (process ID) old priority 0, new priority 10

  
 		 

    
  
 
  Num   12  
 
  ID   task.postalign_bam.bam_to_tag_rep1.line_505.id_21  
 
  Name   bam_to_tag rep1 
 
  Thread   thread_41  
 
  PID   36019  
 
 		  
 
  OK   true   
 
  Exit Code   0   
 
  Retries    
 
  State   FINISHED  
 
  Dep.   OK  
 
  Cpus     
 
  Mem    
 
 		  
 
  Start   2017-01-29 00:48:22  
 
  End   2017-01-29 00:49:36  
 
  Elapsed   00:01:14  
 
  Timeout  00:00:-1 
 
  Wall Timeout   100 days 
 
 		  
 
  Input files  /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H4ac/out/align/rep1/SRR1015998.nodup.bam
   
 
  Output files   /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H4ac/out/align/rep1/SRR1015998.nodup.tagAlign.gz
  
 
  Dependencies     
 
 		  
 
# SYS command. line 507

 if [[ -f $(which conda) && $(conda env list | grep aquas_chipseq | wc -l) != "0" ]]; then source activate aquas_chipseq; sleep 5; fi;  export PATH=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/.:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/modules:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/utils:${PATH}:/bin:/usr/bin:/usr/local/bin:${HOME}/.bds; set -o pipefail; STARTTIME=$(date +%s); renice -n 10 $$

# SYS command. line 510

 bedtools bamtobed -i /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H4ac/out/align/rep1/SRR1015998.nodup.bam | awk 'BEGIN{OFS="\t"}{$4="N";$5="1000";print $0}' | gzip -nc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H4ac/out/align/rep1/SRR1015998.nodup.tagAlign.gz

# SYS command. line 512

 echo

# SYS command. line 514

 TASKTIME=$[$(date +%s)-${STARTTIME}]; if [ ${TASKTIME} -lt 60 ]; then echo "Waiting for $[60-${TASKTIME}] seconds."; sleep $[60-${TASKTIME}]; fi
 
 
   
--------------------Stdout--------------------
52720 (process ID) old priority 0, new priority 10

Waiting for 27 seconds.

  
 		 

    
  
 
  Num   13  
 
  ID   task.postalign_bed.subsample_tag_rep1.line_45.id_22  
 
  Name   subsample_tag rep1 
 
  Thread   thread_41  
 
  PID   36021  
 
 		  
 
  OK   true   
 
  Exit Code   0   
 
  Retries    
 
  State   FINISHED  
 
  Dep.   OK  
 
  Cpus     
 
  Mem    
 
 		  
 
  Start   2017-01-29 00:49:37  
 
  End   2017-01-29 00:50:50  
 
  Elapsed   00:01:13  
 
  Timeout  00:00:-1 
 
  Wall Timeout   100 days 
 
 		  
 
  Input files  /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H4ac/out/align/rep1/SRR1015998.nodup.tagAlign.gz
   
 
  Output files   /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H4ac/out/align/rep1/SRR1015998.nodup.15M.tagAlign.gz
  
 
  Dependencies     
 
 		  
 
# SYS command. line 47

 if [[ -f $(which conda) && $(conda env list | grep aquas_chipseq | wc -l) != "0" ]]; then source activate aquas_chipseq; sleep 5; fi;  export PATH=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/.:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/modules:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/utils:${PATH}:/bin:/usr/bin:/usr/local/bin:${HOME}/.bds; set -o pipefail; STARTTIME=$(date +%s); renice -n 10 $$

# SYS command. line 50

 zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H4ac/out/align/rep1/SRR1015998.nodup.tagAlign.gz | \
			grep -v "chrM" | shuf -n 15000000 --random-source=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H4ac/out/align/rep1/SRR1015998.nodup.tagAlign.gz | gzip -nc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H4ac/out/align/rep1/SRR1015998.nodup.15M.tagAlign.gz

# SYS command. line 53

 TASKTIME=$[$(date +%s)-${STARTTIME}]; if [ ${TASKTIME} -lt 60 ]; then echo "Waiting for $[60-${TASKTIME}] seconds."; sleep $[60-${TASKTIME}]; fi
 
 
   
--------------------Stdout--------------------
583 (process ID) old priority 0, new priority 10
Waiting for 33 seconds.

  
 		 

    
  
 
  Num   14  
 
  ID   task.postalign_bed.spr_rep1.line_255.id_23  
 
  Name   spr rep1 
 
  Thread   thread_41  
 
  PID   36022  
 
 		  
 
  OK   true   
 
  Exit Code   0   
 
  Retries    
 
  State   FINISHED  
 
  Dep.   OK  
 
  Cpus     
 
  Mem    
 
 		  
 
  Start   2017-01-29 00:49:38  
 
  End   2017-01-29 00:50:50  
 
  Elapsed   00:01:12  
 
  Timeout  00:00:-1 
 
  Wall Timeout   100 days 
 
 		  
 
  Input files  /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H4ac/out/align/rep1/SRR1015998.nodup.tagAlign.gz
   
 
  Output files   /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H4ac/out/align/pseudo_reps/rep1/pr1/SRR1015998.nodup.pr1.tagAlign.gz
/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H4ac/out/align/pseudo_reps/rep1/pr2/SRR1015998.nodup.pr2.tagAlign.gz
  
 
  Dependencies     
 
 		  
 
# SYS command. line 257

 if [[ -f $(which conda) && $(conda env list | grep aquas_chipseq | wc -l) != "0" ]]; then source activate aquas_chipseq; sleep 5; fi;  export PATH=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/.:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/modules:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/utils:${PATH}:/bin:/usr/bin:/usr/local/bin:${HOME}/.bds; set -o pipefail; STARTTIME=$(date +%s); renice -n 10 $$

# SYS command. line 260

 nlines=$( zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H4ac/out/align/rep1/SRR1015998.nodup.tagAlign.gz | wc -l )

# SYS command. line 261

 nlines=$(( (nlines + 1) / 2 ))

# SYS command. line 265

 zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H4ac/out/align/rep1/SRR1015998.nodup.tagAlign.gz | shuf --random-source=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H4ac/out/align/rep1/SRR1015998.nodup.tagAlign.gz | split -d -l $((nlines)) - /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H4ac/out/align/pseudo_reps/rep1/pr1/SRR1015998.nodup.

# SYS command. line 268

 gzip -nc /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H4ac/out/align/pseudo_reps/rep1/pr1/SRR1015998.nodup.00 > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H4ac/out/align/pseudo_reps/rep1/pr1/SRR1015998.nodup.pr1.tagAlign.gz

# SYS command. line 269

 rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H4ac/out/align/pseudo_reps/rep1/pr1/SRR1015998.nodup.00

# SYS command. line 270

 gzip -nc /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H4ac/out/align/pseudo_reps/rep1/pr1/SRR1015998.nodup.01 > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H4ac/out/align/pseudo_reps/rep1/pr2/SRR1015998.nodup.pr2.tagAlign.gz

# SYS command. line 271

 rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H4ac/out/align/pseudo_reps/rep1/pr1/SRR1015998.nodup.01

# SYS command. line 273

 TASKTIME=$[$(date +%s)-${STARTTIME}]; if [ ${TASKTIME} -lt 60 ]; then echo "Waiting for $[60-${TASKTIME}] seconds."; sleep $[60-${TASKTIME}]; fi
 
 
   
--------------------Stdout--------------------
582 (process ID) old priority 0, new priority 10
Waiting for 26 seconds.

  
 		 

    
  
 
  Num   15  
 
  ID   task.postalign_bed.xcor_rep1.line_212.id_24  
 
  Name   xcor rep1 
 
  Thread   thread_41  
 
  PID   36023  
 
 		  
 
  OK   true   
 
  Exit Code   0   
 
  Retries    
 
  State   FINISHED  
 
  Dep.   OK  
 
  Cpus    2 
 
  Mem    
 
 		  
 
  Start   2017-01-29 00:50:52  
 
  End   2017-01-29 01:02:00  
 
  Elapsed   00:11:08  
 
  Timeout  00:00:-1 
 
  Wall Timeout   100 days 
 
 		  
 
  Input files  /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H4ac/out/align/rep1/SRR1015998.nodup.15M.tagAlign.gz
   
 
  Output files   /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H4ac/out/qc/rep1/SRR1015998.nodup.15M.cc.qc
/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H4ac/out/qc/rep1/SRR1015998.nodup.15M.cc.plot.pdf
  
 
  Dependencies     
 
 		  
 
# SYS command. line 214

 if [[ -f $(which conda) && $(conda env list | grep aquas_chipseq | wc -l) != "0" ]]; then source activate aquas_chipseq; sleep 5; fi;  export PATH=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/.:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/modules:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/utils:${PATH}:/bin:/usr/bin:/usr/local/bin:${HOME}/.bds; set -o pipefail; STARTTIME=$(date +%s); renice -n 10 $$

# SYS command. line 217

 if [[ $(which run_spp_nodups.R 2> /dev/null | wc -l || echo) == "1" ]]; then RUN_SPP=$(which run_spp_nodups.R); \
		    else RUN_SPP=$(which run_spp.R); \
		    fi

# SYS command. line 223

 Rscript ${RUN_SPP} -rf \
			-c=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H4ac/out/align/rep1/SRR1015998.nodup.15M.tagAlign.gz -p=2 \
			-filtchr=chrM -savp=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H4ac/out/qc/rep1/SRR1015998.nodup.15M.cc.plot.pdf -out=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H4ac/out/qc/rep1/SRR1015998.nodup.15M.cc.qc 

# SYS command. line 226

 sed -r 's/,[^\t]+//g' /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H4ac/out/qc/rep1/SRR1015998.nodup.15M.cc.qc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H4ac/out/qc/rep1/SRR1015998.nodup.15M.cc.qc.tmp

# SYS command. line 227

 mv /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H4ac/out/qc/rep1/SRR1015998.nodup.15M.cc.qc.tmp /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H4ac/out/qc/rep1/SRR1015998.nodup.15M.cc.qc

# SYS command. line 229

 TASKTIME=$[$(date +%s)-${STARTTIME}]; if [ ${TASKTIME} -lt 60 ]; then echo "Waiting for $[60-${TASKTIME}] seconds."; sleep $[60-${TASKTIME}]; fi
 
 
   
--------------------Stdout--------------------
8706 (process ID) old priority 0, new priority 10
################
ChIP data: /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H4ac/out/align/rep1/SRR1015998.nodup.15M.tagAlign.gz 
Control data: NA 
strandshift(min): -500 
strandshift(step): 5 
strandshift(max) 1500 
user-defined peak shift NA 
exclusion(min): 10 
exclusion(max): NaN 
num parallel nodes: 2 
FDR threshold: 0.01 
NumPeaks Threshold: NA 
Output Directory: /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H4ac/out/align/rep1 
narrowPeak output file name: NA 
regionPeak output file name: NA 
Rdata filename: NA 
plot pdf filename: /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H4ac/out/qc/rep1/SRR1015998.nodup.15M.cc.plot.pdf 
result filename: /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H4ac/out/qc/rep1/SRR1015998.nodup.15M.cc.qc 
Overwrite files?: TRUE

Decompressing ChIP file
Reading ChIP tagAlign/BAM file /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H4ac/out/align/rep1/SRR1015998.nodup.15M.tagAlign.gz 
opened /tmp/36023.1.q/RtmpHjMfiq/SRR1015998.nodup.15M.tagAlign224319b5b08d
done. read 15000000 fragments
ChIP data read length 36 
[1] TRUE
Calculating peak characteristics
Minimum cross-correlation value 0.1738531 
Minimum cross-correlation shift 1500 
Top 3 cross-correlation values 0.185785623514677,0.176456210142326,0.176265096521647 
Top 3 estimates for fragment length 100,355,380 
Window half size 260 
Phantom peak location 40 
Phantom peak Correlation 0.182362 
Normalized Strand cross-correlation coefficient (NSC) 1.068635 
Relative Strand cross-correlation Coefficient (RSC) 1.402367 
Phantom Peak Quality Tag 1 
null device 
          1 

 
--------------------Stderr--------------------
Loading required package: caTools

 
 		 

    
  
 
  Num   16  
 
  ID   task.callpeak_macs2.macs2_rep1.line_71.id_25  
 
  Name   macs2 rep1 
 
  Thread   thread_Root  
 
  PID   36040  
 
 		  
 
  OK   true   
 
  Exit Code   0   
 
  Retries    
 
  State   FINISHED  
 
  Dep.   OK  
 
  Cpus     
 
  Mem    
 
 		  
 
  Start   2017-01-29 01:02:02  
 
  End   2017-01-29 01:24:14  
 
  Elapsed   00:22:11  
 
  Timeout  00:00:-1 
 
  Wall Timeout   100 days 
 
 		  
 
  Input files  /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H4ac/out/align/rep1/SRR1015998.nodup.tagAlign.gz
/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H4ac/out/align/ctl1/ENCFF001HNC.nodup.tagAlign.gz
   
 
  Output files   /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H4ac/out/peak/macs2/rep1/SRR1015998.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.narrowPeak.gz
/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H4ac/out/peak/macs2/rep1/SRR1015998.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.gappedPeak.gz
/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H4ac/out/peak/macs2/rep1/SRR1015998.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.broadPeak.gz
/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H4ac/out/signal/macs2/rep1/SRR1015998.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.fc.signal.bw
/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H4ac/out/signal/macs2/rep1/SRR1015998.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.pval.signal.bw
  
 
  Dependencies     
 
 		  
 
# SYS command. line 73

 if [[ -f $(which conda) && $(conda env list | grep aquas_chipseq | wc -l) != "0" ]]; then source activate aquas_chipseq; sleep 5; fi;  export PATH=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/.:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/modules:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/utils:${PATH}:/bin:/usr/bin:/usr/local/bin:${HOME}/.bds; set -o pipefail; STARTTIME=$(date +%s); renice -n 10 $$

# SYS command. line 74

 export LC_COLLATE=C

# SYS command. line 79

 macs2 callpeak -t /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H4ac/out/align/rep1/SRR1015998.nodup.tagAlign.gz -c /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H4ac/out/align/ctl1/ENCFF001HNC.nodup.tagAlign.gz -f BED -n /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H4ac/out/peak/macs2/rep1/SRR1015998.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign -g hs -p 0.01 --nomodel --shift 0 --extsize 100 --keep-dup all -B --SPMR

# SYS command. line 82

 sort -k 8gr,8gr "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H4ac/out/peak/macs2/rep1/SRR1015998.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_peaks.narrowPeak | awk 'BEGIN{OFS="\t"}{$4="Peak_"NR ; print $0}' | gzip -nc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H4ac/out/peak/macs2/rep1/SRR1015998.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.narrowPeak.gz

# SYS command. line 85

 rm -f "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H4ac/out/peak/macs2/rep1/SRR1015998.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_peaks.xls \
			"/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H4ac/out/peak/macs2/rep1/SRR1015998.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_peaks.narrowPeak \
			"/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H4ac/out/peak/macs2/rep1/SRR1015998.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_summits.bed

# SYS command. line 92

 macs2 callpeak -t /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H4ac/out/align/rep1/SRR1015998.nodup.tagAlign.gz -c /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H4ac/out/align/ctl1/ENCFF001HNC.nodup.tagAlign.gz -f BED -n /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H4ac/out/peak/macs2/rep1/SRR1015998.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign -g hs -p 0.01 --broad --nomodel --shift 0 --extsize 100 --keep-dup all

# SYS command. line 95

 sort -k 8gr,8gr "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H4ac/out/peak/macs2/rep1/SRR1015998.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_peaks.broadPeak | awk 'BEGIN{OFS="\t"}{$4="Peak_"NR ; print $0}' | gzip -nc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H4ac/out/peak/macs2/rep1/SRR1015998.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.broadPeak.gz

# SYS command. line 96

 sort -k 14gr,14gr "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H4ac/out/peak/macs2/rep1/SRR1015998.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_peaks.gappedPeak | awk 'BEGIN{OFS="\t"}{$4="Peak_"NR ; print $0}' | gzip -nc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H4ac/out/peak/macs2/rep1/SRR1015998.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.gappedPeak.gz

# SYS command. line 99

 rm -f "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H4ac/out/peak/macs2/rep1/SRR1015998.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_peaks.xls \
		  "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H4ac/out/peak/macs2/rep1/SRR1015998.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_peaks.broadPeak \
		  "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H4ac/out/peak/macs2/rep1/SRR1015998.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_peaks.gappedPeak \
		  "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H4ac/out/peak/macs2/rep1/SRR1015998.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_summits.bed

# SYS command. line 110

 if [[ true == "false" ]]; then \
			rm -f "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H4ac/out/peak/macs2/rep1/SRR1015998.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_treat_pileup.bdg "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H4ac/out/peak/macs2/rep1/SRR1015998.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_control_lambda.bdg; \
			TASKTIME=$[$(date +%s)-${STARTTIME}]; if [ ${TASKTIME} -lt 60 ]; then echo "Waiting for $[60-${TASKTIME}] seconds."; sleep $[60-${TASKTIME}]; fi; \
			exit; \
		fi

# SYS command. line 121

 macs2 bdgcmp -t "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H4ac/out/peak/macs2/rep1/SRR1015998.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_treat_pileup.bdg -c "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H4ac/out/peak/macs2/rep1/SRR1015998.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_control_lambda.bdg --outdir /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H4ac/out/peak/macs2/rep1 -o "SRR1015998.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_FE.bdg -m FE

# SYS command. line 124

 slopBed -i "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H4ac/out/peak/macs2/rep1/SRR1015998.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_FE.bdg -g /mnt/data/bds_pipeline_genome_data/hg38/hg38.chrom.sizes -b 0 |   awk '{if ($3 != -1) print $0}' |  bedClip stdin /mnt/data/bds_pipeline_genome_data/hg38/hg38.chrom.sizes /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H4ac/out/peak/macs2/rep1/SRR1015998.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.fc.signal.bedgraph

# SYS command. line 125

 rm -f "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H4ac/out/peak/macs2/rep1/SRR1015998.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_FE.bdg

# SYS command. line 128

 sort -k1,1 -k2,2n /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H4ac/out/peak/macs2/rep1/SRR1015998.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.fc.signal.bedgraph > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H4ac/out/peak/macs2/rep1/SRR1015998.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.fc.signal.srt.bedgraph

# SYS command. line 129

 bedGraphToBigWig /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H4ac/out/peak/macs2/rep1/SRR1015998.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.fc.signal.srt.bedgraph /mnt/data/bds_pipeline_genome_data/hg38/hg38.chrom.sizes /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H4ac/out/signal/macs2/rep1/SRR1015998.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.fc.signal.bw

# SYS command. line 130

 rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H4ac/out/peak/macs2/rep1/SRR1015998.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.fc.signal.bedgraph /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H4ac/out/peak/macs2/rep1/SRR1015998.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.fc.signal.srt.bedgraph

# SYS command. line 136

 chipReads=$(zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H4ac/out/align/rep1/SRR1015998.nodup.tagAlign.gz | wc -l | awk '{printf "%f", $1/1000000}')

# SYS command. line 138

 controlReads=$(zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H4ac/out/align/ctl1/ENCFF001HNC.nodup.tagAlign.gz | wc -l | awk '{printf "%f", $1/1000000}'); sval=$(echo "${chipReads} ${controlReads}" | awk '$1>$2{printf "%f",$2} $1<=$2{printf "%f",$1}')

# SYS command. line 140

 macs2 bdgcmp -t "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H4ac/out/peak/macs2/rep1/SRR1015998.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_treat_pileup.bdg -c "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H4ac/out/peak/macs2/rep1/SRR1015998.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_control_lambda.bdg --outdir /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H4ac/out/peak/macs2/rep1 -o "SRR1015998.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_ppois.bdg -m ppois -S "${sval}"

# SYS command. line 143

 slopBed -i "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H4ac/out/peak/macs2/rep1/SRR1015998.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_ppois.bdg -g /mnt/data/bds_pipeline_genome_data/hg38/hg38.chrom.sizes -b 0 |   awk '{if ($3 != -1) print $0}' |  bedClip stdin /mnt/data/bds_pipeline_genome_data/hg38/hg38.chrom.sizes /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H4ac/out/peak/macs2/rep1/SRR1015998.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.pval.signal.bedgraph

# SYS command. line 144

 rm -rf "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H4ac/out/peak/macs2/rep1/SRR1015998.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_ppois.bdg

# SYS command. line 147

 sort -k1,1 -k2,2n /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H4ac/out/peak/macs2/rep1/SRR1015998.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.pval.signal.bedgraph > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H4ac/out/peak/macs2/rep1/SRR1015998.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.pval.signal.srt.bedgraph

# SYS command. line 148

 bedGraphToBigWig /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H4ac/out/peak/macs2/rep1/SRR1015998.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.pval.signal.srt.bedgraph /mnt/data/bds_pipeline_genome_data/hg38/hg38.chrom.sizes /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H4ac/out/signal/macs2/rep1/SRR1015998.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.pval.signal.bw

# SYS command. line 149

 rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H4ac/out/peak/macs2/rep1/SRR1015998.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.pval.signal.bedgraph /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H4ac/out/peak/macs2/rep1/SRR1015998.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.pval.signal.srt.bedgraph

# SYS command. line 151

 rm -f "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H4ac/out/peak/macs2/rep1/SRR1015998.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_treat_pileup.bdg "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H4ac/out/peak/macs2/rep1/SRR1015998.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_control_lambda.bdg

# SYS command. line 153

 TASKTIME=$[$(date +%s)-${STARTTIME}]; if [ ${TASKTIME} -lt 60 ]; then echo "Waiting for $[60-${TASKTIME}] seconds."; sleep $[60-${TASKTIME}]; fi
 
 
   
--------------------Stdout--------------------
46027 (process ID) old priority 0, new priority 10

 
--------------------Stderr--------------------
INFO  @ Sun, 29 Jan 2017 01:02:23: 
# Command line: callpeak -t /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H4ac/out/align/rep1/SRR1015998.nodup.tagAlign.gz -c /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H4ac/out/align/ctl1/ENCFF001HNC.nodup.tagAlign.gz -f BED -n /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H4ac/out/peak/macs2/rep1/SRR1015998.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign -g hs -p 0.01 --nomodel --shift 0 --extsize 100 --keep-dup all -B --SPMR
# ARGUMENTS LIST:
# name = /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H4ac/out/peak/macs2/rep1/SRR1015998.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign
# format = BED
# ChIP-seq file = ['/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H4ac/out/align/rep1/SRR1015998.nodup.tagAlign.gz']
# control file = ['/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H4ac/out/align/ctl1/ENCFF001HNC.nodup.tagAlign.gz']
# effective genome size = 2.70e+09
# band width = 300
# model fold = [5, 50]
# pvalue cutoff = 1.00e-02
# qvalue will not be calculated and reported as -1 in the final output.
# Larger dataset will be scaled towards smaller dataset.
# Range for calculating regional lambda is: 1000 bps and 10000 bps
# Broad region calling is off
# MACS will save fragment pileup signal per million reads
 
INFO  @ Sun, 29 Jan 2017 01:02:23: #1 read tag files... 
INFO  @ Sun, 29 Jan 2017 01:02:23: #1 read treatment tags... 
INFO  @ Sun, 29 Jan 2017 01:02:24:  1000000 
INFO  @ Sun, 29 Jan 2017 01:02:26:  2000000 
INFO  @ Sun, 29 Jan 2017 01:02:27:  3000000 
INFO  @ Sun, 29 Jan 2017 01:02:28:  4000000 
INFO  @ Sun, 29 Jan 2017 01:02:30:  5000000 
INFO  @ Sun, 29 Jan 2017 01:02:31:  6000000 
INFO  @ Sun, 29 Jan 2017 01:02:32:  7000000 
INFO  @ Sun, 29 Jan 2017 01:02:34:  8000000 
INFO  @ Sun, 29 Jan 2017 01:02:35:  9000000 
INFO  @ Sun, 29 Jan 2017 01:02:37:  10000000 
INFO  @ Sun, 29 Jan 2017 01:02:38:  11000000 
INFO  @ Sun, 29 Jan 2017 01:02:39:  12000000 
INFO  @ Sun, 29 Jan 2017 01:02:41:  13000000 
INFO  @ Sun, 29 Jan 2017 01:02:42:  14000000 
INFO  @ Sun, 29 Jan 2017 01:02:44:  15000000 
INFO  @ Sun, 29 Jan 2017 01:02:45: #1.2 read input tags... 
INFO  @ Sun, 29 Jan 2017 01:02:46:  1000000 
INFO  @ Sun, 29 Jan 2017 01:02:48:  2000000 
INFO  @ Sun, 29 Jan 2017 01:02:49:  3000000 
INFO  @ Sun, 29 Jan 2017 01:02:50:  4000000 
INFO  @ Sun, 29 Jan 2017 01:02:52:  5000000 
INFO  @ Sun, 29 Jan 2017 01:02:53:  6000000 
INFO  @ Sun, 29 Jan 2017 01:02:55:  7000000 
INFO  @ Sun, 29 Jan 2017 01:02:56:  8000000 
INFO  @ Sun, 29 Jan 2017 01:02:57:  9000000 
INFO  @ Sun, 29 Jan 2017 01:02:59:  10000000 
INFO  @ Sun, 29 Jan 2017 01:03:00:  11000000 
INFO  @ Sun, 29 Jan 2017 01:03:01: #1 tag size is determined as 35 bps 
INFO  @ Sun, 29 Jan 2017 01:03:01: #1 tag size = 35 
INFO  @ Sun, 29 Jan 2017 01:03:01: #1  total tags in treatment: 15735138 
INFO  @ Sun, 29 Jan 2017 01:03:01: #1  total tags in control: 11201413 
INFO  @ Sun, 29 Jan 2017 01:03:01: #1 finished! 
INFO  @ Sun, 29 Jan 2017 01:03:01: #2 Build Peak Model... 
INFO  @ Sun, 29 Jan 2017 01:03:01: #2 Skipped... 
INFO  @ Sun, 29 Jan 2017 01:03:01: #2 Use 100 as fragment length 
INFO  @ Sun, 29 Jan 2017 01:03:01: #3 Call peaks... 
INFO  @ Sun, 29 Jan 2017 01:03:01: #3 Call peaks with given -log10pvalue cutoff: 2.00000 ... 
INFO  @ Sun, 29 Jan 2017 01:03:01: #3 Pre-compute pvalue-qvalue table... 
INFO  @ Sun, 29 Jan 2017 01:03:48: #3 In the peak calling step, the following will be performed simultaneously: 
INFO  @ Sun, 29 Jan 2017 01:03:48: #3   Write bedGraph files for treatment pileup (after scaling if necessary)... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H4ac/out/peak/macs2/rep1/SRR1015998.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign_treat_pileup.bdg 
INFO  @ Sun, 29 Jan 2017 01:03:48: #3   Write bedGraph files for control lambda (after scaling if necessary)... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H4ac/out/peak/macs2/rep1/SRR1015998.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign_control_lambda.bdg 
INFO  @ Sun, 29 Jan 2017 01:03:48: #3   --SPMR is requested, so pileup will be normalized by sequencing depth in million reads. 
INFO  @ Sun, 29 Jan 2017 01:03:48: #3 Call peaks for each chromosome... 
INFO  @ Sun, 29 Jan 2017 01:05:53: #4 Write output xls file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H4ac/out/peak/macs2/rep1/SRR1015998.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign_peaks.xls 
INFO  @ Sun, 29 Jan 2017 01:05:54: #4 Write peak in narrowPeak format file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H4ac/out/peak/macs2/rep1/SRR1015998.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign_peaks.narrowPeak 
INFO  @ Sun, 29 Jan 2017 01:05:54: #4 Write summits bed file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H4ac/out/peak/macs2/rep1/SRR1015998.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign_summits.bed 
INFO  @ Sun, 29 Jan 2017 01:05:54: Done! 
INFO  @ Sun, 29 Jan 2017 01:05:57: 
# Command line: callpeak -t /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H4ac/out/align/rep1/SRR1015998.nodup.tagAlign.gz -c /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H4ac/out/align/ctl1/ENCFF001HNC.nodup.tagAlign.gz -f BED -n /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H4ac/out/peak/macs2/rep1/SRR1015998.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign -g hs -p 0.01 --broad --nomodel --shift 0 --extsize 100 --keep-dup all
# ARGUMENTS LIST:
# name = /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H4ac/out/peak/macs2/rep1/SRR1015998.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign
# format = BED
# ChIP-seq file = ['/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H4ac/out/align/rep1/SRR1015998.nodup.tagAlign.gz']
# control file = ['/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H4ac/out/align/ctl1/ENCFF001HNC.nodup.tagAlign.gz']
# effective genome size = 2.70e+09
# band width = 300
# model fold = [5, 50]
# pvalue cutoff for narrow/strong regions = 1.00e-02
# pvalue cutoff for broad/weak regions = 1.00e-01
# qvalue will not be calculated and reported as -1 in the final output.
# Larger dataset will be scaled towards smaller dataset.
# Range for calculating regional lambda is: 1000 bps and 10000 bps
# Broad region calling is on
 
INFO  @ Sun, 29 Jan 2017 01:05:57: #1 read tag files... 
INFO  @ Sun, 29 Jan 2017 01:05:57: #1 read treatment tags... 
INFO  @ Sun, 29 Jan 2017 01:05:58:  1000000 
INFO  @ Sun, 29 Jan 2017 01:06:00:  2000000 
INFO  @ Sun, 29 Jan 2017 01:06:01:  3000000 
INFO  @ Sun, 29 Jan 2017 01:06:03:  4000000 
INFO  @ Sun, 29 Jan 2017 01:06:04:  5000000 
INFO  @ Sun, 29 Jan 2017 01:06:06:  6000000 
INFO  @ Sun, 29 Jan 2017 01:06:07:  7000000 
INFO  @ Sun, 29 Jan 2017 01:06:09:  8000000 
INFO  @ Sun, 29 Jan 2017 01:06:10:  9000000 
INFO  @ Sun, 29 Jan 2017 01:06:11:  10000000 
INFO  @ Sun, 29 Jan 2017 01:06:13:  11000000 
INFO  @ Sun, 29 Jan 2017 01:06:14:  12000000 
INFO  @ Sun, 29 Jan 2017 01:06:16:  13000000 
INFO  @ Sun, 29 Jan 2017 01:06:17:  14000000 
INFO  @ Sun, 29 Jan 2017 01:06:18:  15000000 
INFO  @ Sun, 29 Jan 2017 01:06:20: #1.2 read input tags... 
INFO  @ Sun, 29 Jan 2017 01:06:21:  1000000 
INFO  @ Sun, 29 Jan 2017 01:06:22:  2000000 
INFO  @ Sun, 29 Jan 2017 01:06:24:  3000000 
INFO  @ Sun, 29 Jan 2017 01:06:25:  4000000 
INFO  @ Sun, 29 Jan 2017 01:06:27:  5000000 
INFO  @ Sun, 29 Jan 2017 01:06:28:  6000000 
INFO  @ Sun, 29 Jan 2017 01:06:30:  7000000 
INFO  @ Sun, 29 Jan 2017 01:06:31:  8000000 
INFO  @ Sun, 29 Jan 2017 01:06:32:  9000000 
INFO  @ Sun, 29 Jan 2017 01:06:34:  10000000 
INFO  @ Sun, 29 Jan 2017 01:06:35:  11000000 
INFO  @ Sun, 29 Jan 2017 01:06:36: #1 tag size is determined as 35 bps 
INFO  @ Sun, 29 Jan 2017 01:06:36: #1 tag size = 35 
INFO  @ Sun, 29 Jan 2017 01:06:36: #1  total tags in treatment: 15735138 
INFO  @ Sun, 29 Jan 2017 01:06:36: #1  total tags in control: 11201413 
INFO  @ Sun, 29 Jan 2017 01:06:36: #1 finished! 
INFO  @ Sun, 29 Jan 2017 01:06:36: #2 Build Peak Model... 
INFO  @ Sun, 29 Jan 2017 01:06:36: #2 Skipped... 
INFO  @ Sun, 29 Jan 2017 01:06:36: #2 Use 100 as fragment length 
INFO  @ Sun, 29 Jan 2017 01:06:36: #3 Call peaks... 
INFO  @ Sun, 29 Jan 2017 01:06:36: #3 Call broad peaks with given level1 -log10pvalue cutoff and level2: 2.00000, 1.00000... 
INFO  @ Sun, 29 Jan 2017 01:06:36: #3 Pre-compute pvalue-qvalue table... 
INFO  @ Sun, 29 Jan 2017 01:07:23: #3 Call peaks for each chromosome... 
INFO  @ Sun, 29 Jan 2017 01:08:12: #4 Write output xls file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H4ac/out/peak/macs2/rep1/SRR1015998.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign_peaks.xls 
INFO  @ Sun, 29 Jan 2017 01:08:17: #4 Write broad peak in broadPeak format file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H4ac/out/peak/macs2/rep1/SRR1015998.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign_peaks.broadPeak 
INFO  @ Sun, 29 Jan 2017 01:08:20: #4 Write broad peak in bed12/gappedPeak format file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H4ac/out/peak/macs2/rep1/SRR1015998.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign_peaks.gappedPeak 
INFO  @ Sun, 29 Jan 2017 01:08:23: Done! 
INFO  @ Sun, 29 Jan 2017 01:08:32: Read and build treatment bedGraph... 
INFO  @ Sun, 29 Jan 2017 01:09:03: Read and build control bedGraph... 
INFO  @ Sun, 29 Jan 2017 01:09:35: Build scoreTrackII... 
INFO  @ Sun, 29 Jan 2017 01:09:53: Calculate scores comparing treatment and control by 'FE'... 
INFO  @ Sun, 29 Jan 2017 01:12:06: Write bedGraph of scores... 
INFO  @ Sun, 29 Jan 2017 01:13:29: Finished 'FE'! Please check '/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H4ac/out/peak/macs2/rep1/SRR1015998.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign_FE.bdg'! 
INFO  @ Sun, 29 Jan 2017 01:16:20: Read and build treatment bedGraph... 
INFO  @ Sun, 29 Jan 2017 01:16:51: Read and build control bedGraph... 
INFO  @ Sun, 29 Jan 2017 01:17:24: Build scoreTrackII... 
INFO  @ Sun, 29 Jan 2017 01:17:41: Values in your input bedGraph files will be multiplied by 11.201413 ... 
INFO  @ Sun, 29 Jan 2017 01:19:55: Calculate scores comparing treatment and control by 'ppois'... 
INFO  @ Sun, 29 Jan 2017 01:20:12: Write bedGraph of scores... 
INFO  @ Sun, 29 Jan 2017 01:21:21: Finished 'ppois'! Please check '/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H4ac/out/peak/macs2/rep1/SRR1015998.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign_ppois.bdg'! 

 
 		 

    
  
 
  Num   17  
 
  ID   task.callpeak_macs2.macs2_rep1_pr1.line_71.id_26  
 
  Name   macs2 rep1-pr1 
 
  Thread   thread_Root  
 
  PID   36041  
 
 		  
 
  OK   true   
 
  Exit Code   0   
 
  Retries    
 
  State   FINISHED  
 
  Dep.   OK  
 
  Cpus     
 
  Mem    
 
 		  
 
  Start   2017-01-29 01:02:03  
 
  End   2017-01-29 01:08:10  
 
  Elapsed   00:06:07  
 
  Timeout  00:00:-1 
 
  Wall Timeout   100 days 
 
 		  
 
  Input files  /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H4ac/out/align/pseudo_reps/rep1/pr1/SRR1015998.nodup.pr1.tagAlign.gz
/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H4ac/out/align/ctl1/ENCFF001HNC.nodup.tagAlign.gz
   
 
  Output files   /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H4ac/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1015998.nodup.pr1.tagAlign_x_ENCFF001HNC.nodup.tagAlign.narrowPeak.gz
/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H4ac/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1015998.nodup.pr1.tagAlign_x_ENCFF001HNC.nodup.tagAlign.gappedPeak.gz
/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H4ac/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1015998.nodup.pr1.tagAlign_x_ENCFF001HNC.nodup.tagAlign.broadPeak.gz
  
 
  Dependencies     
 
 		  
 
# SYS command. line 73

 if [[ -f $(which conda) && $(conda env list | grep aquas_chipseq | wc -l) != "0" ]]; then source activate aquas_chipseq; sleep 5; fi;  export PATH=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/.:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/modules:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/utils:${PATH}:/bin:/usr/bin:/usr/local/bin:${HOME}/.bds; set -o pipefail; STARTTIME=$(date +%s); renice -n 10 $$

# SYS command. line 74

 export LC_COLLATE=C

# SYS command. line 79

 macs2 callpeak -t /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H4ac/out/align/pseudo_reps/rep1/pr1/SRR1015998.nodup.pr1.tagAlign.gz -c /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H4ac/out/align/ctl1/ENCFF001HNC.nodup.tagAlign.gz -f BED -n /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H4ac/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1015998.nodup.pr1.tagAlign_x_ENCFF001HNC.nodup.tagAlign -g hs -p 0.01 --nomodel --shift 0 --extsize 100 --keep-dup all -B --SPMR

# SYS command. line 82

 sort -k 8gr,8gr "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H4ac/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1015998.nodup.pr1.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_peaks.narrowPeak | awk 'BEGIN{OFS="\t"}{$4="Peak_"NR ; print $0}' | gzip -nc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H4ac/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1015998.nodup.pr1.tagAlign_x_ENCFF001HNC.nodup.tagAlign.narrowPeak.gz

# SYS command. line 85

 rm -f "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H4ac/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1015998.nodup.pr1.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_peaks.xls \
			"/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H4ac/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1015998.nodup.pr1.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_peaks.narrowPeak \
			"/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H4ac/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1015998.nodup.pr1.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_summits.bed

# SYS command. line 92

 macs2 callpeak -t /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H4ac/out/align/pseudo_reps/rep1/pr1/SRR1015998.nodup.pr1.tagAlign.gz -c /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H4ac/out/align/ctl1/ENCFF001HNC.nodup.tagAlign.gz -f BED -n /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H4ac/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1015998.nodup.pr1.tagAlign_x_ENCFF001HNC.nodup.tagAlign -g hs -p 0.01 --broad --nomodel --shift 0 --extsize 100 --keep-dup all

# SYS command. line 95

 sort -k 8gr,8gr "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H4ac/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1015998.nodup.pr1.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_peaks.broadPeak | awk 'BEGIN{OFS="\t"}{$4="Peak_"NR ; print $0}' | gzip -nc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H4ac/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1015998.nodup.pr1.tagAlign_x_ENCFF001HNC.nodup.tagAlign.broadPeak.gz

# SYS command. line 96

 sort -k 14gr,14gr "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H4ac/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1015998.nodup.pr1.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_peaks.gappedPeak | awk 'BEGIN{OFS="\t"}{$4="Peak_"NR ; print $0}' | gzip -nc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H4ac/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1015998.nodup.pr1.tagAlign_x_ENCFF001HNC.nodup.tagAlign.gappedPeak.gz

# SYS command. line 99

 rm -f "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H4ac/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1015998.nodup.pr1.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_peaks.xls \
		  "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H4ac/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1015998.nodup.pr1.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_peaks.broadPeak \
		  "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H4ac/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1015998.nodup.pr1.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_peaks.gappedPeak \
		  "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H4ac/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1015998.nodup.pr1.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_summits.bed

# SYS command. line 110

 if [[ false == "false" ]]; then \
			rm -f "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H4ac/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1015998.nodup.pr1.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_treat_pileup.bdg "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H4ac/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1015998.nodup.pr1.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_control_lambda.bdg; \
			TASKTIME=$[$(date +%s)-${STARTTIME}]; if [ ${TASKTIME} -lt 60 ]; then echo "Waiting for $[60-${TASKTIME}] seconds."; sleep $[60-${TASKTIME}]; fi; \
			exit; \
		fi

# SYS command. line 121

 macs2 bdgcmp -t "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H4ac/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1015998.nodup.pr1.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_treat_pileup.bdg -c "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H4ac/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1015998.nodup.pr1.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_control_lambda.bdg --outdir /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H4ac/out/peak/macs2/pseudo_reps/rep1/pr1 -o "SRR1015998.nodup.pr1.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_FE.bdg -m FE

# SYS command. line 124

 slopBed -i "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H4ac/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1015998.nodup.pr1.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_FE.bdg -g /mnt/data/bds_pipeline_genome_data/hg38/hg38.chrom.sizes -b 0 |   awk '{if ($3 != -1) print $0}' |  bedClip stdin /mnt/data/bds_pipeline_genome_data/hg38/hg38.chrom.sizes /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H4ac/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1015998.nodup.pr1.tagAlign_x_ENCFF001HNC.nodup.tagAlign.fc.signal.bedgraph

# SYS command. line 125

 rm -f "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H4ac/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1015998.nodup.pr1.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_FE.bdg

# SYS command. line 128

 sort -k1,1 -k2,2n /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H4ac/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1015998.nodup.pr1.tagAlign_x_ENCFF001HNC.nodup.tagAlign.fc.signal.bedgraph > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H4ac/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1015998.nodup.pr1.tagAlign_x_ENCFF001HNC.nodup.tagAlign.fc.signal.srt.bedgraph

# SYS command. line 129

 bedGraphToBigWig /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H4ac/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1015998.nodup.pr1.tagAlign_x_ENCFF001HNC.nodup.tagAlign.fc.signal.srt.bedgraph /mnt/data/bds_pipeline_genome_data/hg38/hg38.chrom.sizes /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H4ac/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1015998.nodup.pr1.tagAlign_x_ENCFF001HNC.nodup.tagAlign.fc.signal.bw

# SYS command. line 130

 rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H4ac/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1015998.nodup.pr1.tagAlign_x_ENCFF001HNC.nodup.tagAlign.fc.signal.bedgraph /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H4ac/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1015998.nodup.pr1.tagAlign_x_ENCFF001HNC.nodup.tagAlign.fc.signal.srt.bedgraph

# SYS command. line 136

 chipReads=$(zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H4ac/out/align/pseudo_reps/rep1/pr1/SRR1015998.nodup.pr1.tagAlign.gz | wc -l | awk '{printf "%f", $1/1000000}')

# SYS command. line 138

 controlReads=$(zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H4ac/out/align/ctl1/ENCFF001HNC.nodup.tagAlign.gz | wc -l | awk '{printf "%f", $1/1000000}'); sval=$(echo "${chipReads} ${controlReads}" | awk '$1>$2{printf "%f",$2} $1<=$2{printf "%f",$1}')

# SYS command. line 140

 macs2 bdgcmp -t "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H4ac/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1015998.nodup.pr1.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_treat_pileup.bdg -c "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H4ac/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1015998.nodup.pr1.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_control_lambda.bdg --outdir /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H4ac/out/peak/macs2/pseudo_reps/rep1/pr1 -o "SRR1015998.nodup.pr1.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_ppois.bdg -m ppois -S "${sval}"

# SYS command. line 143

 slopBed -i "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H4ac/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1015998.nodup.pr1.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_ppois.bdg -g /mnt/data/bds_pipeline_genome_data/hg38/hg38.chrom.sizes -b 0 |   awk '{if ($3 != -1) print $0}' |  bedClip stdin /mnt/data/bds_pipeline_genome_data/hg38/hg38.chrom.sizes /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H4ac/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1015998.nodup.pr1.tagAlign_x_ENCFF001HNC.nodup.tagAlign.pval.signal.bedgraph

# SYS command. line 144

 rm -rf "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H4ac/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1015998.nodup.pr1.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_ppois.bdg

# SYS command. line 147

 sort -k1,1 -k2,2n /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H4ac/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1015998.nodup.pr1.tagAlign_x_ENCFF001HNC.nodup.tagAlign.pval.signal.bedgraph > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H4ac/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1015998.nodup.pr1.tagAlign_x_ENCFF001HNC.nodup.tagAlign.pval.signal.srt.bedgraph

# SYS command. line 148

 bedGraphToBigWig /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H4ac/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1015998.nodup.pr1.tagAlign_x_ENCFF001HNC.nodup.tagAlign.pval.signal.srt.bedgraph /mnt/data/bds_pipeline_genome_data/hg38/hg38.chrom.sizes /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H4ac/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1015998.nodup.pr1.tagAlign_x_ENCFF001HNC.nodup.tagAlign.pval.signal.bw

# SYS command. line 149

 rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H4ac/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1015998.nodup.pr1.tagAlign_x_ENCFF001HNC.nodup.tagAlign.pval.signal.bedgraph /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H4ac/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1015998.nodup.pr1.tagAlign_x_ENCFF001HNC.nodup.tagAlign.pval.signal.srt.bedgraph

# SYS command. line 151

 rm -f "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H4ac/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1015998.nodup.pr1.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_treat_pileup.bdg "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H4ac/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1015998.nodup.pr1.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_control_lambda.bdg

# SYS command. line 153

 TASKTIME=$[$(date +%s)-${STARTTIME}]; if [ ${TASKTIME} -lt 60 ]; then echo "Waiting for $[60-${TASKTIME}] seconds."; sleep $[60-${TASKTIME}]; fi
 
 
   
--------------------Stdout--------------------
46026 (process ID) old priority 0, new priority 10

 
--------------------Stderr--------------------
INFO  @ Sun, 29 Jan 2017 01:02:23: 
# Command line: callpeak -t /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H4ac/out/align/pseudo_reps/rep1/pr1/SRR1015998.nodup.pr1.tagAlign.gz -c /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H4ac/out/align/ctl1/ENCFF001HNC.nodup.tagAlign.gz -f BED -n /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H4ac/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1015998.nodup.pr1.tagAlign_x_ENCFF001HNC.nodup.tagAlign -g hs -p 0.01 --nomodel --shift 0 --extsize 100 --keep-dup all -B --SPMR
# ARGUMENTS LIST:
# name = /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H4ac/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1015998.nodup.pr1.tagAlign_x_ENCFF001HNC.nodup.tagAlign
# format = BED
# ChIP-seq file = ['/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H4ac/out/align/pseudo_reps/rep1/pr1/SRR1015998.nodup.pr1.tagAlign.gz']
# control file = ['/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H4ac/out/align/ctl1/ENCFF001HNC.nodup.tagAlign.gz']
# effective genome size = 2.70e+09
# band width = 300
# model fold = [5, 50]
# pvalue cutoff = 1.00e-02
# qvalue will not be calculated and reported as -1 in the final output.
# Larger dataset will be scaled towards smaller dataset.
# Range for calculating regional lambda is: 1000 bps and 10000 bps
# Broad region calling is off
# MACS will save fragment pileup signal per million reads
 
INFO  @ Sun, 29 Jan 2017 01:02:23: #1 read tag files... 
INFO  @ Sun, 29 Jan 2017 01:02:23: #1 read treatment tags... 
INFO  @ Sun, 29 Jan 2017 01:02:24:  1000000 
INFO  @ Sun, 29 Jan 2017 01:02:26:  2000000 
INFO  @ Sun, 29 Jan 2017 01:02:27:  3000000 
INFO  @ Sun, 29 Jan 2017 01:02:29:  4000000 
INFO  @ Sun, 29 Jan 2017 01:02:30:  5000000 
INFO  @ Sun, 29 Jan 2017 01:02:32:  6000000 
INFO  @ Sun, 29 Jan 2017 01:02:33:  7000000 
INFO  @ Sun, 29 Jan 2017 01:02:35: #1.2 read input tags... 
INFO  @ Sun, 29 Jan 2017 01:02:37:  1000000 
INFO  @ Sun, 29 Jan 2017 01:02:38:  2000000 
INFO  @ Sun, 29 Jan 2017 01:02:39:  3000000 
INFO  @ Sun, 29 Jan 2017 01:02:41:  4000000 
INFO  @ Sun, 29 Jan 2017 01:02:42:  5000000 
INFO  @ Sun, 29 Jan 2017 01:02:44:  6000000 
INFO  @ Sun, 29 Jan 2017 01:02:45:  7000000 
INFO  @ Sun, 29 Jan 2017 01:02:46:  8000000 
INFO  @ Sun, 29 Jan 2017 01:02:48:  9000000 
INFO  @ Sun, 29 Jan 2017 01:02:49:  10000000 
INFO  @ Sun, 29 Jan 2017 01:02:50:  11000000 
INFO  @ Sun, 29 Jan 2017 01:02:51: #1 tag size is determined as 35 bps 
INFO  @ Sun, 29 Jan 2017 01:02:51: #1 tag size = 35 
INFO  @ Sun, 29 Jan 2017 01:02:51: #1  total tags in treatment: 7867569 
INFO  @ Sun, 29 Jan 2017 01:02:51: #1  total tags in control: 11201413 
INFO  @ Sun, 29 Jan 2017 01:02:51: #1 finished! 
INFO  @ Sun, 29 Jan 2017 01:02:51: #2 Build Peak Model... 
INFO  @ Sun, 29 Jan 2017 01:02:51: #2 Skipped... 
INFO  @ Sun, 29 Jan 2017 01:02:51: #2 Use 100 as fragment length 
INFO  @ Sun, 29 Jan 2017 01:02:51: #3 Call peaks... 
INFO  @ Sun, 29 Jan 2017 01:02:51: #3 Call peaks with given -log10pvalue cutoff: 2.00000 ... 
INFO  @ Sun, 29 Jan 2017 01:02:51: #3 Pre-compute pvalue-qvalue table... 
INFO  @ Sun, 29 Jan 2017 01:03:30: #3 In the peak calling step, the following will be performed simultaneously: 
INFO  @ Sun, 29 Jan 2017 01:03:30: #3   Write bedGraph files for treatment pileup (after scaling if necessary)... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H4ac/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1015998.nodup.pr1.tagAlign_x_ENCFF001HNC.nodup.tagAlign_treat_pileup.bdg 
INFO  @ Sun, 29 Jan 2017 01:03:30: #3   Write bedGraph files for control lambda (after scaling if necessary)... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H4ac/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1015998.nodup.pr1.tagAlign_x_ENCFF001HNC.nodup.tagAlign_control_lambda.bdg 
INFO  @ Sun, 29 Jan 2017 01:03:30: #3   --SPMR is requested, so pileup will be normalized by sequencing depth in million reads. 
INFO  @ Sun, 29 Jan 2017 01:03:30: #3 Call peaks for each chromosome... 
INFO  @ Sun, 29 Jan 2017 01:05:09: #4 Write output xls file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H4ac/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1015998.nodup.pr1.tagAlign_x_ENCFF001HNC.nodup.tagAlign_peaks.xls 
INFO  @ Sun, 29 Jan 2017 01:05:10: #4 Write peak in narrowPeak format file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H4ac/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1015998.nodup.pr1.tagAlign_x_ENCFF001HNC.nodup.tagAlign_peaks.narrowPeak 
INFO  @ Sun, 29 Jan 2017 01:05:11: #4 Write summits bed file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H4ac/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1015998.nodup.pr1.tagAlign_x_ENCFF001HNC.nodup.tagAlign_summits.bed 
INFO  @ Sun, 29 Jan 2017 01:05:12: Done! 
INFO  @ Sun, 29 Jan 2017 01:05:15: 
# Command line: callpeak -t /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H4ac/out/align/pseudo_reps/rep1/pr1/SRR1015998.nodup.pr1.tagAlign.gz -c /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H4ac/out/align/ctl1/ENCFF001HNC.nodup.tagAlign.gz -f BED -n /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H4ac/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1015998.nodup.pr1.tagAlign_x_ENCFF001HNC.nodup.tagAlign -g hs -p 0.01 --broad --nomodel --shift 0 --extsize 100 --keep-dup all
# ARGUMENTS LIST:
# name = /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H4ac/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1015998.nodup.pr1.tagAlign_x_ENCFF001HNC.nodup.tagAlign
# format = BED
# ChIP-seq file = ['/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H4ac/out/align/pseudo_reps/rep1/pr1/SRR1015998.nodup.pr1.tagAlign.gz']
# control file = ['/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H4ac/out/align/ctl1/ENCFF001HNC.nodup.tagAlign.gz']
# effective genome size = 2.70e+09
# band width = 300
# model fold = [5, 50]
# pvalue cutoff for narrow/strong regions = 1.00e-02
# pvalue cutoff for broad/weak regions = 1.00e-01
# qvalue will not be calculated and reported as -1 in the final output.
# Larger dataset will be scaled towards smaller dataset.
# Range for calculating regional lambda is: 1000 bps and 10000 bps
# Broad region calling is on
 
INFO  @ Sun, 29 Jan 2017 01:05:15: #1 read tag files... 
INFO  @ Sun, 29 Jan 2017 01:05:15: #1 read treatment tags... 
INFO  @ Sun, 29 Jan 2017 01:05:17:  1000000 
INFO  @ Sun, 29 Jan 2017 01:05:18:  2000000 
INFO  @ Sun, 29 Jan 2017 01:05:20:  3000000 
INFO  @ Sun, 29 Jan 2017 01:05:21:  4000000 
INFO  @ Sun, 29 Jan 2017 01:05:23:  5000000 
INFO  @ Sun, 29 Jan 2017 01:05:24:  6000000 
INFO  @ Sun, 29 Jan 2017 01:05:26:  7000000 
INFO  @ Sun, 29 Jan 2017 01:05:28: #1.2 read input tags... 
INFO  @ Sun, 29 Jan 2017 01:05:29:  1000000 
INFO  @ Sun, 29 Jan 2017 01:05:30:  2000000 
INFO  @ Sun, 29 Jan 2017 01:05:32:  3000000 
INFO  @ Sun, 29 Jan 2017 01:05:33:  4000000 
INFO  @ Sun, 29 Jan 2017 01:05:34:  5000000 
INFO  @ Sun, 29 Jan 2017 01:05:36:  6000000 
INFO  @ Sun, 29 Jan 2017 01:05:37:  7000000 
INFO  @ Sun, 29 Jan 2017 01:05:39:  8000000 
INFO  @ Sun, 29 Jan 2017 01:05:40:  9000000 
INFO  @ Sun, 29 Jan 2017 01:05:41:  10000000 
INFO  @ Sun, 29 Jan 2017 01:05:43:  11000000 
INFO  @ Sun, 29 Jan 2017 01:05:43: #1 tag size is determined as 35 bps 
INFO  @ Sun, 29 Jan 2017 01:05:43: #1 tag size = 35 
INFO  @ Sun, 29 Jan 2017 01:05:43: #1  total tags in treatment: 7867569 
INFO  @ Sun, 29 Jan 2017 01:05:43: #1  total tags in control: 11201413 
INFO  @ Sun, 29 Jan 2017 01:05:43: #1 finished! 
INFO  @ Sun, 29 Jan 2017 01:05:43: #2 Build Peak Model... 
INFO  @ Sun, 29 Jan 2017 01:05:43: #2 Skipped... 
INFO  @ Sun, 29 Jan 2017 01:05:43: #2 Use 100 as fragment length 
INFO  @ Sun, 29 Jan 2017 01:05:43: #3 Call peaks... 
INFO  @ Sun, 29 Jan 2017 01:05:43: #3 Call broad peaks with given level1 -log10pvalue cutoff and level2: 2.00000, 1.00000... 
INFO  @ Sun, 29 Jan 2017 01:05:43: #3 Pre-compute pvalue-qvalue table... 
INFO  @ Sun, 29 Jan 2017 01:06:33: #3 Call peaks for each chromosome... 
INFO  @ Sun, 29 Jan 2017 01:07:37: #4 Write output xls file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H4ac/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1015998.nodup.pr1.tagAlign_x_ENCFF001HNC.nodup.tagAlign_peaks.xls 
INFO  @ Sun, 29 Jan 2017 01:07:46: #4 Write broad peak in broadPeak format file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H4ac/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1015998.nodup.pr1.tagAlign_x_ENCFF001HNC.nodup.tagAlign_peaks.broadPeak 
INFO  @ Sun, 29 Jan 2017 01:07:51: #4 Write broad peak in bed12/gappedPeak format file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H4ac/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1015998.nodup.pr1.tagAlign_x_ENCFF001HNC.nodup.tagAlign_peaks.gappedPeak 
INFO  @ Sun, 29 Jan 2017 01:07:55: Done! 

 
 		 

    
  
 
  Num   18  
 
  ID   task.callpeak_macs2.macs2_rep1_pr2.line_71.id_27  
 
  Name   macs2 rep1-pr2 
 
  Thread   thread_Root  
 
  PID   36042  
 
 		  
 
  OK   true   
 
  Exit Code   0   
 
  Retries    
 
  State   FINISHED  
 
  Dep.   OK  
 
  Cpus     
 
  Mem    
 
 		  
 
  Start   2017-01-29 01:02:04  
 
  End   2017-01-29 01:08:01  
 
  Elapsed   00:05:56  
 
  Timeout  00:00:-1 
 
  Wall Timeout   100 days 
 
 		  
 
  Input files  /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H4ac/out/align/pseudo_reps/rep1/pr2/SRR1015998.nodup.pr2.tagAlign.gz
/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H4ac/out/align/ctl1/ENCFF001HNC.nodup.tagAlign.gz
   
 
  Output files   /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H4ac/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1015998.nodup.pr2.tagAlign_x_ENCFF001HNC.nodup.tagAlign.narrowPeak.gz
/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H4ac/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1015998.nodup.pr2.tagAlign_x_ENCFF001HNC.nodup.tagAlign.gappedPeak.gz
/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H4ac/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1015998.nodup.pr2.tagAlign_x_ENCFF001HNC.nodup.tagAlign.broadPeak.gz
  
 
  Dependencies     
 
 		  
 
# SYS command. line 73

 if [[ -f $(which conda) && $(conda env list | grep aquas_chipseq | wc -l) != "0" ]]; then source activate aquas_chipseq; sleep 5; fi;  export PATH=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/.:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/modules:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/utils:${PATH}:/bin:/usr/bin:/usr/local/bin:${HOME}/.bds; set -o pipefail; STARTTIME=$(date +%s); renice -n 10 $$

# SYS command. line 74

 export LC_COLLATE=C

# SYS command. line 79

 macs2 callpeak -t /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H4ac/out/align/pseudo_reps/rep1/pr2/SRR1015998.nodup.pr2.tagAlign.gz -c /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H4ac/out/align/ctl1/ENCFF001HNC.nodup.tagAlign.gz -f BED -n /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H4ac/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1015998.nodup.pr2.tagAlign_x_ENCFF001HNC.nodup.tagAlign -g hs -p 0.01 --nomodel --shift 0 --extsize 100 --keep-dup all -B --SPMR

# SYS command. line 82

 sort -k 8gr,8gr "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H4ac/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1015998.nodup.pr2.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_peaks.narrowPeak | awk 'BEGIN{OFS="\t"}{$4="Peak_"NR ; print $0}' | gzip -nc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H4ac/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1015998.nodup.pr2.tagAlign_x_ENCFF001HNC.nodup.tagAlign.narrowPeak.gz

# SYS command. line 85

 rm -f "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H4ac/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1015998.nodup.pr2.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_peaks.xls \
			"/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H4ac/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1015998.nodup.pr2.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_peaks.narrowPeak \
			"/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H4ac/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1015998.nodup.pr2.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_summits.bed

# SYS command. line 92

 macs2 callpeak -t /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H4ac/out/align/pseudo_reps/rep1/pr2/SRR1015998.nodup.pr2.tagAlign.gz -c /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H4ac/out/align/ctl1/ENCFF001HNC.nodup.tagAlign.gz -f BED -n /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H4ac/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1015998.nodup.pr2.tagAlign_x_ENCFF001HNC.nodup.tagAlign -g hs -p 0.01 --broad --nomodel --shift 0 --extsize 100 --keep-dup all

# SYS command. line 95

 sort -k 8gr,8gr "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H4ac/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1015998.nodup.pr2.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_peaks.broadPeak | awk 'BEGIN{OFS="\t"}{$4="Peak_"NR ; print $0}' | gzip -nc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H4ac/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1015998.nodup.pr2.tagAlign_x_ENCFF001HNC.nodup.tagAlign.broadPeak.gz

# SYS command. line 96

 sort -k 14gr,14gr "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H4ac/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1015998.nodup.pr2.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_peaks.gappedPeak | awk 'BEGIN{OFS="\t"}{$4="Peak_"NR ; print $0}' | gzip -nc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H4ac/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1015998.nodup.pr2.tagAlign_x_ENCFF001HNC.nodup.tagAlign.gappedPeak.gz

# SYS command. line 99

 rm -f "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H4ac/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1015998.nodup.pr2.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_peaks.xls \
		  "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H4ac/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1015998.nodup.pr2.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_peaks.broadPeak \
		  "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H4ac/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1015998.nodup.pr2.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_peaks.gappedPeak \
		  "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H4ac/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1015998.nodup.pr2.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_summits.bed

# SYS command. line 110

 if [[ false == "false" ]]; then \
			rm -f "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H4ac/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1015998.nodup.pr2.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_treat_pileup.bdg "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H4ac/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1015998.nodup.pr2.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_control_lambda.bdg; \
			TASKTIME=$[$(date +%s)-${STARTTIME}]; if [ ${TASKTIME} -lt 60 ]; then echo "Waiting for $[60-${TASKTIME}] seconds."; sleep $[60-${TASKTIME}]; fi; \
			exit; \
		fi

# SYS command. line 121

 macs2 bdgcmp -t "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H4ac/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1015998.nodup.pr2.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_treat_pileup.bdg -c "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H4ac/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1015998.nodup.pr2.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_control_lambda.bdg --outdir /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H4ac/out/peak/macs2/pseudo_reps/rep1/pr2 -o "SRR1015998.nodup.pr2.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_FE.bdg -m FE

# SYS command. line 124

 slopBed -i "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H4ac/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1015998.nodup.pr2.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_FE.bdg -g /mnt/data/bds_pipeline_genome_data/hg38/hg38.chrom.sizes -b 0 |   awk '{if ($3 != -1) print $0}' |  bedClip stdin /mnt/data/bds_pipeline_genome_data/hg38/hg38.chrom.sizes /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H4ac/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1015998.nodup.pr2.tagAlign_x_ENCFF001HNC.nodup.tagAlign.fc.signal.bedgraph

# SYS command. line 125

 rm -f "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H4ac/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1015998.nodup.pr2.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_FE.bdg

# SYS command. line 128

 sort -k1,1 -k2,2n /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H4ac/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1015998.nodup.pr2.tagAlign_x_ENCFF001HNC.nodup.tagAlign.fc.signal.bedgraph > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H4ac/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1015998.nodup.pr2.tagAlign_x_ENCFF001HNC.nodup.tagAlign.fc.signal.srt.bedgraph

# SYS command. line 129

 bedGraphToBigWig /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H4ac/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1015998.nodup.pr2.tagAlign_x_ENCFF001HNC.nodup.tagAlign.fc.signal.srt.bedgraph /mnt/data/bds_pipeline_genome_data/hg38/hg38.chrom.sizes /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H4ac/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1015998.nodup.pr2.tagAlign_x_ENCFF001HNC.nodup.tagAlign.fc.signal.bw

# SYS command. line 130

 rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H4ac/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1015998.nodup.pr2.tagAlign_x_ENCFF001HNC.nodup.tagAlign.fc.signal.bedgraph /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H4ac/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1015998.nodup.pr2.tagAlign_x_ENCFF001HNC.nodup.tagAlign.fc.signal.srt.bedgraph

# SYS command. line 136

 chipReads=$(zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H4ac/out/align/pseudo_reps/rep1/pr2/SRR1015998.nodup.pr2.tagAlign.gz | wc -l | awk '{printf "%f", $1/1000000}')

# SYS command. line 138

 controlReads=$(zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H4ac/out/align/ctl1/ENCFF001HNC.nodup.tagAlign.gz | wc -l | awk '{printf "%f", $1/1000000}'); sval=$(echo "${chipReads} ${controlReads}" | awk '$1>$2{printf "%f",$2} $1<=$2{printf "%f",$1}')

# SYS command. line 140

 macs2 bdgcmp -t "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H4ac/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1015998.nodup.pr2.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_treat_pileup.bdg -c "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H4ac/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1015998.nodup.pr2.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_control_lambda.bdg --outdir /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H4ac/out/peak/macs2/pseudo_reps/rep1/pr2 -o "SRR1015998.nodup.pr2.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_ppois.bdg -m ppois -S "${sval}"

# SYS command. line 143

 slopBed -i "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H4ac/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1015998.nodup.pr2.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_ppois.bdg -g /mnt/data/bds_pipeline_genome_data/hg38/hg38.chrom.sizes -b 0 |   awk '{if ($3 != -1) print $0}' |  bedClip stdin /mnt/data/bds_pipeline_genome_data/hg38/hg38.chrom.sizes /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H4ac/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1015998.nodup.pr2.tagAlign_x_ENCFF001HNC.nodup.tagAlign.pval.signal.bedgraph

# SYS command. line 144

 rm -rf "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H4ac/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1015998.nodup.pr2.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_ppois.bdg

# SYS command. line 147

 sort -k1,1 -k2,2n /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H4ac/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1015998.nodup.pr2.tagAlign_x_ENCFF001HNC.nodup.tagAlign.pval.signal.bedgraph > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H4ac/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1015998.nodup.pr2.tagAlign_x_ENCFF001HNC.nodup.tagAlign.pval.signal.srt.bedgraph

# SYS command. line 148

 bedGraphToBigWig /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H4ac/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1015998.nodup.pr2.tagAlign_x_ENCFF001HNC.nodup.tagAlign.pval.signal.srt.bedgraph /mnt/data/bds_pipeline_genome_data/hg38/hg38.chrom.sizes /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H4ac/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1015998.nodup.pr2.tagAlign_x_ENCFF001HNC.nodup.tagAlign.pval.signal.bw

# SYS command. line 149

 rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H4ac/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1015998.nodup.pr2.tagAlign_x_ENCFF001HNC.nodup.tagAlign.pval.signal.bedgraph /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H4ac/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1015998.nodup.pr2.tagAlign_x_ENCFF001HNC.nodup.tagAlign.pval.signal.srt.bedgraph

# SYS command. line 151

 rm -f "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H4ac/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1015998.nodup.pr2.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_treat_pileup.bdg "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H4ac/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1015998.nodup.pr2.tagAlign_x_ENCFF001HNC.nodup.tagAlign"_control_lambda.bdg

# SYS command. line 153

 TASKTIME=$[$(date +%s)-${STARTTIME}]; if [ ${TASKTIME} -lt 60 ]; then echo "Waiting for $[60-${TASKTIME}] seconds."; sleep $[60-${TASKTIME}]; fi
 
 
   
--------------------Stdout--------------------
46025 (process ID) old priority 0, new priority 10

 
--------------------Stderr--------------------
INFO  @ Sun, 29 Jan 2017 01:02:23: 
# Command line: callpeak -t /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H4ac/out/align/pseudo_reps/rep1/pr2/SRR1015998.nodup.pr2.tagAlign.gz -c /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H4ac/out/align/ctl1/ENCFF001HNC.nodup.tagAlign.gz -f BED -n /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H4ac/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1015998.nodup.pr2.tagAlign_x_ENCFF001HNC.nodup.tagAlign -g hs -p 0.01 --nomodel --shift 0 --extsize 100 --keep-dup all -B --SPMR
# ARGUMENTS LIST:
# name = /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H4ac/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1015998.nodup.pr2.tagAlign_x_ENCFF001HNC.nodup.tagAlign
# format = BED
# ChIP-seq file = ['/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H4ac/out/align/pseudo_reps/rep1/pr2/SRR1015998.nodup.pr2.tagAlign.gz']
# control file = ['/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H4ac/out/align/ctl1/ENCFF001HNC.nodup.tagAlign.gz']
# effective genome size = 2.70e+09
# band width = 300
# model fold = [5, 50]
# pvalue cutoff = 1.00e-02
# qvalue will not be calculated and reported as -1 in the final output.
# Larger dataset will be scaled towards smaller dataset.
# Range for calculating regional lambda is: 1000 bps and 10000 bps
# Broad region calling is off
# MACS will save fragment pileup signal per million reads
 
INFO  @ Sun, 29 Jan 2017 01:02:23: #1 read tag files... 
INFO  @ Sun, 29 Jan 2017 01:02:23: #1 read treatment tags... 
INFO  @ Sun, 29 Jan 2017 01:02:24:  1000000 
INFO  @ Sun, 29 Jan 2017 01:02:26:  2000000 
INFO  @ Sun, 29 Jan 2017 01:02:27:  3000000 
INFO  @ Sun, 29 Jan 2017 01:02:29:  4000000 
INFO  @ Sun, 29 Jan 2017 01:02:31:  5000000 
INFO  @ Sun, 29 Jan 2017 01:02:33:  6000000 
INFO  @ Sun, 29 Jan 2017 01:02:34:  7000000 
INFO  @ Sun, 29 Jan 2017 01:02:36: #1.2 read input tags... 
INFO  @ Sun, 29 Jan 2017 01:02:37:  1000000 
INFO  @ Sun, 29 Jan 2017 01:02:39:  2000000 
INFO  @ Sun, 29 Jan 2017 01:02:40:  3000000 
INFO  @ Sun, 29 Jan 2017 01:02:41:  4000000 
INFO  @ Sun, 29 Jan 2017 01:02:43:  5000000 
INFO  @ Sun, 29 Jan 2017 01:02:44:  6000000 
INFO  @ Sun, 29 Jan 2017 01:02:46:  7000000 
INFO  @ Sun, 29 Jan 2017 01:02:47:  8000000 
INFO  @ Sun, 29 Jan 2017 01:02:48:  9000000 
INFO  @ Sun, 29 Jan 2017 01:02:50:  10000000 
INFO  @ Sun, 29 Jan 2017 01:02:51:  11000000 
INFO  @ Sun, 29 Jan 2017 01:02:52: #1 tag size is determined as 35 bps 
INFO  @ Sun, 29 Jan 2017 01:02:52: #1 tag size = 35 
INFO  @ Sun, 29 Jan 2017 01:02:52: #1  total tags in treatment: 7867569 
INFO  @ Sun, 29 Jan 2017 01:02:52: #1  total tags in control: 11201413 
INFO  @ Sun, 29 Jan 2017 01:02:52: #1 finished! 
INFO  @ Sun, 29 Jan 2017 01:02:52: #2 Build Peak Model... 
INFO  @ Sun, 29 Jan 2017 01:02:52: #2 Skipped... 
INFO  @ Sun, 29 Jan 2017 01:02:52: #2 Use 100 as fragment length 
INFO  @ Sun, 29 Jan 2017 01:02:52: #3 Call peaks... 
INFO  @ Sun, 29 Jan 2017 01:02:52: #3 Call peaks with given -log10pvalue cutoff: 2.00000 ... 
INFO  @ Sun, 29 Jan 2017 01:02:52: #3 Pre-compute pvalue-qvalue table... 
INFO  @ Sun, 29 Jan 2017 01:03:30: #3 In the peak calling step, the following will be performed simultaneously: 
INFO  @ Sun, 29 Jan 2017 01:03:30: #3   Write bedGraph files for treatment pileup (after scaling if necessary)... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H4ac/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1015998.nodup.pr2.tagAlign_x_ENCFF001HNC.nodup.tagAlign_treat_pileup.bdg 
INFO  @ Sun, 29 Jan 2017 01:03:30: #3   Write bedGraph files for control lambda (after scaling if necessary)... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H4ac/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1015998.nodup.pr2.tagAlign_x_ENCFF001HNC.nodup.tagAlign_control_lambda.bdg 
INFO  @ Sun, 29 Jan 2017 01:03:30: #3   --SPMR is requested, so pileup will be normalized by sequencing depth in million reads. 
INFO  @ Sun, 29 Jan 2017 01:03:30: #3 Call peaks for each chromosome... 
INFO  @ Sun, 29 Jan 2017 01:05:09: #4 Write output xls file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H4ac/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1015998.nodup.pr2.tagAlign_x_ENCFF001HNC.nodup.tagAlign_peaks.xls 
INFO  @ Sun, 29 Jan 2017 01:05:10: #4 Write peak in narrowPeak format file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H4ac/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1015998.nodup.pr2.tagAlign_x_ENCFF001HNC.nodup.tagAlign_peaks.narrowPeak 
INFO  @ Sun, 29 Jan 2017 01:05:11: #4 Write summits bed file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H4ac/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1015998.nodup.pr2.tagAlign_x_ENCFF001HNC.nodup.tagAlign_summits.bed 
INFO  @ Sun, 29 Jan 2017 01:05:12: Done! 
INFO  @ Sun, 29 Jan 2017 01:05:15: 
# Command line: callpeak -t /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H4ac/out/align/pseudo_reps/rep1/pr2/SRR1015998.nodup.pr2.tagAlign.gz -c /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H4ac/out/align/ctl1/ENCFF001HNC.nodup.tagAlign.gz -f BED -n /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H4ac/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1015998.nodup.pr2.tagAlign_x_ENCFF001HNC.nodup.tagAlign -g hs -p 0.01 --broad --nomodel --shift 0 --extsize 100 --keep-dup all
# ARGUMENTS LIST:
# name = /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H4ac/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1015998.nodup.pr2.tagAlign_x_ENCFF001HNC.nodup.tagAlign
# format = BED
# ChIP-seq file = ['/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H4ac/out/align/pseudo_reps/rep1/pr2/SRR1015998.nodup.pr2.tagAlign.gz']
# control file = ['/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H4ac/out/align/ctl1/ENCFF001HNC.nodup.tagAlign.gz']
# effective genome size = 2.70e+09
# band width = 300
# model fold = [5, 50]
# pvalue cutoff for narrow/strong regions = 1.00e-02
# pvalue cutoff for broad/weak regions = 1.00e-01
# qvalue will not be calculated and reported as -1 in the final output.
# Larger dataset will be scaled towards smaller dataset.
# Range for calculating regional lambda is: 1000 bps and 10000 bps
# Broad region calling is on
 
INFO  @ Sun, 29 Jan 2017 01:05:15: #1 read tag files... 
INFO  @ Sun, 29 Jan 2017 01:05:15: #1 read treatment tags... 
INFO  @ Sun, 29 Jan 2017 01:05:17:  1000000 
INFO  @ Sun, 29 Jan 2017 01:05:18:  2000000 
INFO  @ Sun, 29 Jan 2017 01:05:20:  3000000 
INFO  @ Sun, 29 Jan 2017 01:05:21:  4000000 
INFO  @ Sun, 29 Jan 2017 01:05:23:  5000000 
INFO  @ Sun, 29 Jan 2017 01:05:24:  6000000 
INFO  @ Sun, 29 Jan 2017 01:05:26:  7000000 
INFO  @ Sun, 29 Jan 2017 01:05:28: #1.2 read input tags... 
INFO  @ Sun, 29 Jan 2017 01:05:29:  1000000 
INFO  @ Sun, 29 Jan 2017 01:05:30:  2000000 
INFO  @ Sun, 29 Jan 2017 01:05:32:  3000000 
INFO  @ Sun, 29 Jan 2017 01:05:33:  4000000 
INFO  @ Sun, 29 Jan 2017 01:05:35:  5000000 
INFO  @ Sun, 29 Jan 2017 01:05:36:  6000000 
INFO  @ Sun, 29 Jan 2017 01:05:38:  7000000 
INFO  @ Sun, 29 Jan 2017 01:05:39:  8000000 
INFO  @ Sun, 29 Jan 2017 01:05:40:  9000000 
INFO  @ Sun, 29 Jan 2017 01:05:42:  10000000 
INFO  @ Sun, 29 Jan 2017 01:05:43:  11000000 
INFO  @ Sun, 29 Jan 2017 01:05:44: #1 tag size is determined as 35 bps 
INFO  @ Sun, 29 Jan 2017 01:05:44: #1 tag size = 35 
INFO  @ Sun, 29 Jan 2017 01:05:44: #1  total tags in treatment: 7867569 
INFO  @ Sun, 29 Jan 2017 01:05:44: #1  total tags in control: 11201413 
INFO  @ Sun, 29 Jan 2017 01:05:44: #1 finished! 
INFO  @ Sun, 29 Jan 2017 01:05:44: #2 Build Peak Model... 
INFO  @ Sun, 29 Jan 2017 01:05:44: #2 Skipped... 
INFO  @ Sun, 29 Jan 2017 01:05:44: #2 Use 100 as fragment length 
INFO  @ Sun, 29 Jan 2017 01:05:44: #3 Call peaks... 
INFO  @ Sun, 29 Jan 2017 01:05:44: #3 Call broad peaks with given level1 -log10pvalue cutoff and level2: 2.00000, 1.00000... 
INFO  @ Sun, 29 Jan 2017 01:05:44: #3 Pre-compute pvalue-qvalue table... 
INFO  @ Sun, 29 Jan 2017 01:06:24: #3 Call peaks for each chromosome... 
INFO  @ Sun, 29 Jan 2017 01:07:27: #4 Write output xls file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H4ac/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1015998.nodup.pr2.tagAlign_x_ENCFF001HNC.nodup.tagAlign_peaks.xls 
INFO  @ Sun, 29 Jan 2017 01:07:35: #4 Write broad peak in broadPeak format file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H4ac/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1015998.nodup.pr2.tagAlign_x_ENCFF001HNC.nodup.tagAlign_peaks.broadPeak 
INFO  @ Sun, 29 Jan 2017 01:07:40: #4 Write broad peak in bed12/gappedPeak format file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H4ac/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1015998.nodup.pr2.tagAlign_x_ENCFF001HNC.nodup.tagAlign_peaks.gappedPeak 
INFO  @ Sun, 29 Jan 2017 01:07:45: Done! 

 
 		 

    
  
 
  Num   19  
 
  ID   task.callpeak_naive_overlap.naive_overlap_thresh.line_59.id_28  
 
  Name   naive_overlap_thresh  
 
  Thread   thread_Root  
 
  PID   36059  
 
 		  
 
  OK   true   
 
  Exit Code   0   
 
  Retries    
 
  State   FINISHED  
 
  Dep.   OK  
 
  Cpus     
 
  Mem    
 
 		  
 
  Start   2017-01-29 01:24:15  
 
  End   2017-01-29 01:25:37  
 
  Elapsed   00:01:21  
 
  Timeout  01:00:00 
 
  Wall Timeout   100 days 
 
 		  
 
  Input files  /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H4ac/out/peak/macs2/rep1/SRR1015998.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.narrowPeak.gz
/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H4ac/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1015998.nodup.pr1.tagAlign_x_ENCFF001HNC.nodup.tagAlign.narrowPeak.gz
/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H4ac/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1015998.nodup.pr2.tagAlign_x_ENCFF001HNC.nodup.tagAlign.narrowPeak.gz
   
 
  Output files   /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H4ac/out/peak/macs2/overlap/SRR1015998.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.naive_overlap.filt.narrowPeak.gz
  
 
  Dependencies     
 
 		  
 
# SYS command. line 61

 if [[ -f $(which conda) && $(conda env list | grep aquas_chipseq | wc -l) != "0" ]]; then source activate aquas_chipseq; sleep 5; fi;  export PATH=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/.:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/modules:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/utils:${PATH}:/bin:/usr/bin:/usr/local/bin:${HOME}/.bds; set -o pipefail; STARTTIME=$(date +%s); renice -n 10 $$

# SYS command. line 64

 intersectBed  -wo -a <(zcat -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H4ac/out/peak/macs2/rep1/SRR1015998.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.narrowPeak.gz) -b <(zcat -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H4ac/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1015998.nodup.pr1.tagAlign_x_ENCFF001HNC.nodup.tagAlign.narrowPeak.gz) | \
			awk 'BEGIN{FS="\t";OFS="\t"} {s1=$3-$2; s2=$13-$12; if (($21/s1 >= 0.5) || ($21/s2 >= 0.5)) {print $0}}' | cut -f 1-10 | sort | uniq | \
			intersectBed  -wo -a stdin -b <(zcat -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H4ac/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1015998.nodup.pr2.tagAlign_x_ENCFF001HNC.nodup.tagAlign.narrowPeak.gz) | \
			awk 'BEGIN{FS="\t";OFS="\t"} {s1=$3-$2; s2=$13-$12; if (($21/s1 >= 0.5) || ($21/s2 >= 0.5)) {print $0}}' | cut -f 1-10 | sort | uniq | gzip -nc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H4ac/out/peak/macs2/overlap/SRR1015998.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.PooledInRep1AndRep2.narrowPeak.gz

# SYS command. line 70

 zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H4ac/out/peak/macs2/overlap/SRR1015998.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.PooledInRep1AndRep2.narrowPeak.gz | sort | uniq | gzip -nc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H4ac/out/peak/macs2/overlap/SRR1015998.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.naive_overlap.narrowPeak.gz

# SYS command. line 72

 bedtools intersect -v -a /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H4ac/out/peak/macs2/overlap/SRR1015998.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.naive_overlap.narrowPeak.gz -b /mnt/data/annotations/by_release/hg20.GRCh38/hg38.blacklist.bed.gz  | grep -P 'chr[\dXY]+[ \t]' | awk 'BEGIN{OFS="\t"} {if ($5>1000) $5=1000; print $0}' | gzip -nc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H4ac/out/peak/macs2/overlap/SRR1015998.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.naive_overlap.filt.narrowPeak.gz

# SYS command. line 74

 rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H4ac/out/peak/macs2/overlap/SRR1015998.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.PooledInRep1AndRep2.narrowPeak.gz

# SYS command. line 76

 TASKTIME=$[$(date +%s)-${STARTTIME}]; if [ ${TASKTIME} -lt 60 ]; then echo "Waiting for $[60-${TASKTIME}] seconds."; sleep $[60-${TASKTIME}]; fi
 
 
   
--------------------Stdout--------------------
9972 (process ID) old priority 0, new priority 10
Waiting for 57 seconds.

 
--------------------Stderr--------------------
***** WARNING: File /dev/fd/62 has inconsistent naming convention for record:
KI270830.1	16859	17130	Peak_1535	108	.	7.04898	10.80254	6.27448	95

***** WARNING: File /dev/fd/62 has inconsistent naming convention for record:
KI270830.1	16859	17130	Peak_1535	108	.	7.04898	10.80254	6.27448	95

***** WARNING: File /dev/fd/63 has inconsistent naming convention for record:
KI270729.1	2492	2608	Peak_2062	97	.	4.41100	9.79108	5.40367	61

***** WARNING: File /dev/fd/63 has inconsistent naming convention for record:
KI270729.1	2492	2608	Peak_2062	97	.	4.41100	9.79108	5.40367	61

***** WARNING: File /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H4ac/out/peak/macs2/overlap/SRR1015998.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.naive_overlap.narrowPeak.gz has inconsistent naming convention for record:
GL000008.2	4126	4281	Peak_10780	52	.	3.01416	5.26630	1.70182	105

***** WARNING: File /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H4ac/out/peak/macs2/overlap/SRR1015998.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.naive_overlap.narrowPeak.gz has inconsistent naming convention for record:
GL000008.2	4126	4281	Peak_10780	52	.	3.01416	5.26630	1.70182	105


 
 		 

    
  
 
  Num   20  
 
  ID   task.callpeak_naive_overlap.naive_overlap_thresh.line_59.id_29  
 
  Name   naive_overlap_thresh  
 
  Thread   thread_Root  
 
  PID   36060  
 
 		  
 
  OK   true   
 
  Exit Code   0   
 
  Retries    
 
  State   FINISHED  
 
  Dep.   OK  
 
  Cpus     
 
  Mem    
 
 		  
 
  Start   2017-01-29 01:24:16  
 
  End   2017-01-29 01:25:37  
 
  Elapsed   00:01:20  
 
  Timeout  01:00:00 
 
  Wall Timeout   100 days 
 
 		  
 
  Input files  /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H4ac/out/peak/macs2/rep1/SRR1015998.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.gappedPeak.gz
/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H4ac/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1015998.nodup.pr1.tagAlign_x_ENCFF001HNC.nodup.tagAlign.gappedPeak.gz
/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H4ac/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1015998.nodup.pr2.tagAlign_x_ENCFF001HNC.nodup.tagAlign.gappedPeak.gz
   
 
  Output files   /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H4ac/out/peak/macs2/overlap/SRR1015998.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.naive_overlap.filt.gappedPeak.gz
  
 
  Dependencies     
 
 		  
 
# SYS command. line 61

 if [[ -f $(which conda) && $(conda env list | grep aquas_chipseq | wc -l) != "0" ]]; then source activate aquas_chipseq; sleep 5; fi;  export PATH=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/.:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/modules:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/utils:${PATH}:/bin:/usr/bin:/usr/local/bin:${HOME}/.bds; set -o pipefail; STARTTIME=$(date +%s); renice -n 10 $$

# SYS command. line 64

 intersectBed  -wo -a <(zcat -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H4ac/out/peak/macs2/rep1/SRR1015998.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.gappedPeak.gz) -b <(zcat -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H4ac/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1015998.nodup.pr1.tagAlign_x_ENCFF001HNC.nodup.tagAlign.gappedPeak.gz) | \
			awk 'BEGIN{FS="\t";OFS="\t"} {s1=$3-$2; s2=$18-$17; if (($31/s1 >= 0.5) || ($31/s2 >= 0.5)) {print $0}}' | cut -f 1-15 | sort | uniq | \
			intersectBed  -wo -a stdin -b <(zcat -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H4ac/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1015998.nodup.pr2.tagAlign_x_ENCFF001HNC.nodup.tagAlign.gappedPeak.gz) | \
			awk 'BEGIN{FS="\t";OFS="\t"} {s1=$3-$2; s2=$18-$17; if (($31/s1 >= 0.5) || ($31/s2 >= 0.5)) {print $0}}' | cut -f 1-15 | sort | uniq | gzip -nc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H4ac/out/peak/macs2/overlap/SRR1015998.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.PooledInRep1AndRep2.gappedPeak.gz

# SYS command. line 70

 zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H4ac/out/peak/macs2/overlap/SRR1015998.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.PooledInRep1AndRep2.gappedPeak.gz | sort | uniq | gzip -nc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H4ac/out/peak/macs2/overlap/SRR1015998.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.naive_overlap.gappedPeak.gz

# SYS command. line 72

 bedtools intersect -v -a /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H4ac/out/peak/macs2/overlap/SRR1015998.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.naive_overlap.gappedPeak.gz -b /mnt/data/annotations/by_release/hg20.GRCh38/hg38.blacklist.bed.gz  | grep -P 'chr[\dXY]+[ \t]' | awk 'BEGIN{OFS="\t"} {if ($5>1000) $5=1000; print $0}' | gzip -nc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H4ac/out/peak/macs2/overlap/SRR1015998.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.naive_overlap.filt.gappedPeak.gz

# SYS command. line 74

 rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H4ac/out/peak/macs2/overlap/SRR1015998.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.PooledInRep1AndRep2.gappedPeak.gz

# SYS command. line 76

 TASKTIME=$[$(date +%s)-${STARTTIME}]; if [ ${TASKTIME} -lt 60 ]; then echo "Waiting for $[60-${TASKTIME}] seconds."; sleep $[60-${TASKTIME}]; fi
 
 
   
--------------------Stdout--------------------
12437 (process ID) old priority 0, new priority 10
Waiting for 29 seconds.

 
--------------------Stderr--------------------
***** WARNING: File /dev/fd/62 has inconsistent naming convention for record:
GL000195.1	55001	55101	Peak_954	35	.	55001	55101	0	2	1,1	0,99	5.42051	7.56160	3.50989

***** WARNING: File /dev/fd/62 has inconsistent naming convention for record:
GL000195.1	55001	55101	Peak_954	35	.	55001	55101	0	2	1,1	0,99	5.42051	7.56160	3.50989

***** WARNING: File /dev/fd/63 has inconsistent naming convention for record:
GL000008.2	168368	168468	Peak_3541	14	.	168368	168468	0	2	1,1	0,99	3.74260	4.77671	1.45644

***** WARNING: File /dev/fd/63 has inconsistent naming convention for record:
GL000008.2	168368	168468	Peak_3541	14	.	168368	168468	0	2	1,1	0,99	3.74260	4.77671	1.45644

***** WARNING: File /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H4ac/out/peak/macs2/overlap/SRR1015998.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.naive_overlap.gappedPeak.gz has inconsistent naming convention for record:
GL000008.2	0	907	Peak_61395	0	.	0	907	0	2	1,1	0,906	1.94412	1.51968	0.00000

***** WARNING: File /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H4ac/out/peak/macs2/overlap/SRR1015998.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.naive_overlap.gappedPeak.gz has inconsistent naming convention for record:
GL000008.2	0	907	Peak_61395	0	.	0	907	0	2	1,1	0,906	1.94412	1.51968	0.00000


 
 		 

    
  
 
  Num   21  
 
  ID   task.callpeak_naive_overlap.naive_overlap_thresh.line_59.id_30  
 
  Name   naive_overlap_thresh  
 
  Thread   thread_Root  
 
  PID   36061  
 
 		  
 
  OK   true   
 
  Exit Code   0   
 
  Retries    
 
  State   FINISHED  
 
  Dep.   OK  
 
  Cpus     
 
  Mem    
 
 		  
 
  Start   2017-01-29 01:24:18  
 
  End   2017-01-29 01:25:37  
 
  Elapsed   00:01:19  
 
  Timeout  01:00:00 
 
  Wall Timeout   100 days 
 
 		  
 
  Input files  /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H4ac/out/peak/macs2/rep1/SRR1015998.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.broadPeak.gz
/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H4ac/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1015998.nodup.pr1.tagAlign_x_ENCFF001HNC.nodup.tagAlign.broadPeak.gz
/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H4ac/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1015998.nodup.pr2.tagAlign_x_ENCFF001HNC.nodup.tagAlign.broadPeak.gz
   
 
  Output files   /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H4ac/out/peak/macs2/overlap/SRR1015998.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.naive_overlap.filt.broadPeak.gz
  
 
  Dependencies     
 
 		  
 
# SYS command. line 61

 if [[ -f $(which conda) && $(conda env list | grep aquas_chipseq | wc -l) != "0" ]]; then source activate aquas_chipseq; sleep 5; fi;  export PATH=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/.:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/modules:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/utils:${PATH}:/bin:/usr/bin:/usr/local/bin:${HOME}/.bds; set -o pipefail; STARTTIME=$(date +%s); renice -n 10 $$

# SYS command. line 64

 intersectBed  -wo -a <(zcat -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H4ac/out/peak/macs2/rep1/SRR1015998.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.broadPeak.gz) -b <(zcat -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H4ac/out/peak/macs2/pseudo_reps/rep1/pr1/SRR1015998.nodup.pr1.tagAlign_x_ENCFF001HNC.nodup.tagAlign.broadPeak.gz) | \
			awk 'BEGIN{FS="\t";OFS="\t"} {s1=$3-$2; s2=$12-$11; if (($19/s1 >= 0.5) || ($19/s2 >= 0.5)) {print $0}}' | cut -f 1-9 | sort | uniq | \
			intersectBed  -wo -a stdin -b <(zcat -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H4ac/out/peak/macs2/pseudo_reps/rep1/pr2/SRR1015998.nodup.pr2.tagAlign_x_ENCFF001HNC.nodup.tagAlign.broadPeak.gz) | \
			awk 'BEGIN{FS="\t";OFS="\t"} {s1=$3-$2; s2=$12-$11; if (($19/s1 >= 0.5) || ($19/s2 >= 0.5)) {print $0}}' | cut -f 1-9 | sort | uniq | gzip -nc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H4ac/out/peak/macs2/overlap/SRR1015998.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.PooledInRep1AndRep2.broadPeak.gz

# SYS command. line 70

 zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H4ac/out/peak/macs2/overlap/SRR1015998.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.PooledInRep1AndRep2.broadPeak.gz | sort | uniq | gzip -nc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H4ac/out/peak/macs2/overlap/SRR1015998.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.naive_overlap.broadPeak.gz

# SYS command. line 72

 bedtools intersect -v -a /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H4ac/out/peak/macs2/overlap/SRR1015998.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.naive_overlap.broadPeak.gz -b /mnt/data/annotations/by_release/hg20.GRCh38/hg38.blacklist.bed.gz  | grep -P 'chr[\dXY]+[ \t]' | awk 'BEGIN{OFS="\t"} {if ($5>1000) $5=1000; print $0}' | gzip -nc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H4ac/out/peak/macs2/overlap/SRR1015998.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.naive_overlap.filt.broadPeak.gz

# SYS command. line 74

 rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H4ac/out/peak/macs2/overlap/SRR1015998.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.PooledInRep1AndRep2.broadPeak.gz

# SYS command. line 76

 TASKTIME=$[$(date +%s)-${STARTTIME}]; if [ ${TASKTIME} -lt 60 ]; then echo "Waiting for $[60-${TASKTIME}] seconds."; sleep $[60-${TASKTIME}]; fi
 
 
   
--------------------Stdout--------------------
9973 (process ID) old priority 0, new priority 10
Waiting for 36 seconds.

 
--------------------Stderr--------------------
***** WARNING: File /dev/fd/62 has inconsistent naming convention for record:
GL000195.1	55001	55101	Peak_954	35	.	5.42051	7.56160	3.50989

***** WARNING: File /dev/fd/62 has inconsistent naming convention for record:
GL000195.1	55001	55101	Peak_954	35	.	5.42051	7.56160	3.50989

***** WARNING: File /dev/fd/63 has inconsistent naming convention for record:
GL000008.2	168368	168468	Peak_3541	14	.	3.74260	4.77671	1.45644

***** WARNING: File /dev/fd/63 has inconsistent naming convention for record:
GL000008.2	168368	168468	Peak_3541	14	.	3.74260	4.77671	1.45644

***** WARNING: File /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H4ac/out/peak/macs2/overlap/SRR1015998.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.naive_overlap.broadPeak.gz has inconsistent naming convention for record:
GL000008.2	0	907	Peak_61395	0	.	1.94412	1.51968	0.00000

***** WARNING: File /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H4ac/out/peak/macs2/overlap/SRR1015998.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.naive_overlap.broadPeak.gz has inconsistent naming convention for record:
GL000008.2	0	907	Peak_61395	0	.	1.94412	1.51968	0.00000


 
 		 

    
  
 
  Num   22  
 
  ID   task.callpeak_blacklist_filter.blacklist_filter_peak_1.line_27.id_31  
 
  Name   blacklist_filter peak 1 
 
  Thread   thread_Root  
 
  PID   16914  
 
 		  
 
  OK   true   
 
  Exit Code   0   
 
  Retries    
 
  State   FINISHED  
 
  Dep.   OK  
 
  Cpus     
 
  Mem    
 
 		  
 
  Start   2017-01-29 01:25:39  
 
  End   2017-01-29 01:26:48  
 
  Elapsed   00:01:09  
 
  Timeout  00:00:-1 
 
  Wall Timeout   100 days 
 
 		  
 
  Input files  /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H4ac/out/peak/macs2/rep1/SRR1015998.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.narrowPeak.gz
   
 
  Output files   /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H4ac/out/peak/macs2/rep1/SRR1015998.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.filt.narrowPeak.gz
  
 
  Dependencies     
 
 		  
 
# SYS command. line 29

 if [[ -f $(which conda) && $(conda env list | grep aquas_chipseq | wc -l) != "0" ]]; then source activate aquas_chipseq; sleep 5; fi;  export PATH=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/.:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/modules:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/utils:${PATH}:/bin:/usr/bin:/usr/local/bin:${HOME}/.bds; set -o pipefail; STARTTIME=$(date +%s); renice -n 10 $$

# SYS command. line 31

 bedtools intersect -v -a /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H4ac/out/peak/macs2/rep1/SRR1015998.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.narrowPeak.gz -b /mnt/data/annotations/by_release/hg20.GRCh38/hg38.blacklist.bed.gz \
			| awk 'BEGIN{OFS="\t"} {if ($5>1000) $5=1000; print $0}' \
			| grep -P 'chr[\dXY]+[ \t]' | gzip -nc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H4ac/out/peak/macs2/rep1/SRR1015998.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.filt.narrowPeak.gz

# SYS command. line 35

 TASKTIME=$[$(date +%s)-${STARTTIME}]; if [ ${TASKTIME} -lt 60 ]; then echo "Waiting for $[60-${TASKTIME}] seconds."; sleep $[60-${TASKTIME}]; fi
 
 
   
--------------------Stdout--------------------
16918 (process ID) old priority 0, new priority 10
Waiting for 60 seconds.

 
--------------------Stderr--------------------
***** WARNING: File /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H4ac/out/peak/macs2/rep1/SRR1015998.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.narrowPeak.gz has inconsistent naming convention for record:
KI270830.1	16862	17141	Peak_1728	113	.	7.26279	11.34488	6.92937	94

***** WARNING: File /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H4ac/out/peak/macs2/rep1/SRR1015998.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.narrowPeak.gz has inconsistent naming convention for record:
KI270830.1	16862	17141	Peak_1728	113	.	7.26279	11.34488	6.92937	94


 
 		 

    
  
 
  Num   23  
 
  ID   task.report.peak2hammock.line_412.id_32  
 
  Name   peak2hammock 
 
  Thread   thread_Root  
 
  PID   21266  
 
 		  
 
  OK   true   
 
  Exit Code   0   
 
  Retries    
 
  State   FINISHED  
 
  Dep.   OK  
 
  Cpus     
 
  Mem    
 
 		  
 
  Start   2017-01-29 01:26:49  
 
  End   2017-01-29 01:26:58  
 
  Elapsed   00:00:09  
 
  Timeout  00:00:-1 
 
  Wall Timeout   100 days 
 
 		  
 
  Input files  /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H4ac/out/peak/macs2/overlap/SRR1015998.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.naive_overlap.filt.narrowPeak.gz
   
 
  Output files   /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H4ac/out/peak/macs2/overlap/SRR1015998.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.naive_overlap.filt.narrowPeak.hammock.gz
  
 
  Dependencies     
 
 		  
 
# SYS command. line 414

 if [[ -f $(which conda) && $(conda env list | grep aquas_chipseq | wc -l) != "0" ]]; then source activate aquas_chipseq; sleep 5; fi;  export PATH=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/.:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/modules:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/utils:${PATH}:/bin:/usr/bin:/usr/local/bin:${HOME}/.bds; set -o pipefail; STARTTIME=$(date +%s); renice -n 10 $$

# SYS command. line 415

 zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H4ac/out/peak/macs2/overlap/SRR1015998.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.naive_overlap.filt.narrowPeak.gz | sed '/^\(chr\)/!d' | sort -k1,1V -k2,2n > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H4ac/out/peak/macs2/overlap/SRR1015998.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.naive_overlap.filt.narrowPeak.tmp

# SYS command. line 417

 /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/utils/narrowpeak.py /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H4ac/out/peak/macs2/overlap/SRR1015998.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.naive_overlap.filt.narrowPeak.tmp /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H4ac/out/peak/macs2/overlap/SRR1015998.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.naive_overlap.filt.narrowPeak.hammock

# SYS command. line 418

 rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H4ac/out/peak/macs2/overlap/SRR1015998.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.naive_overlap.filt.narrowPeak.tmp
 
 
   
--------------------Stdout--------------------
21270 (process ID) old priority 0, new priority 10

  
 		 

    
  
 
  Num   24  
 
  ID   task.report.peak2hammock.line_412.id_33  
 
  Name   peak2hammock 
 
  Thread   thread_Root  
 
  PID   21834  
 
 		  
 
  OK   true   
 
  Exit Code   0   
 
  Retries    
 
  State   FINISHED  
 
  Dep.   OK  
 
  Cpus     
 
  Mem    
 
 		  
 
  Start   2017-01-29 01:26:59  
 
  End   2017-01-29 01:27:18  
 
  Elapsed   00:00:19  
 
  Timeout  00:00:-1 
 
  Wall Timeout   100 days 
 
 		  
 
  Input files  /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H4ac/out/peak/macs2/overlap/SRR1015998.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.naive_overlap.filt.gappedPeak.gz
   
 
  Output files   /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H4ac/out/peak/macs2/overlap/SRR1015998.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.naive_overlap.filt.gappedPeak.hammock.gz
  
 
  Dependencies     
 
 		  
 
# SYS command. line 414

 if [[ -f $(which conda) && $(conda env list | grep aquas_chipseq | wc -l) != "0" ]]; then source activate aquas_chipseq; sleep 5; fi;  export PATH=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/.:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/modules:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/utils:${PATH}:/bin:/usr/bin:/usr/local/bin:${HOME}/.bds; set -o pipefail; STARTTIME=$(date +%s); renice -n 10 $$

# SYS command. line 415

 zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H4ac/out/peak/macs2/overlap/SRR1015998.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.naive_overlap.filt.gappedPeak.gz | sed '/^\(chr\)/!d' | sort -k1,1V -k2,2n > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H4ac/out/peak/macs2/overlap/SRR1015998.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.naive_overlap.filt.gappedPeak.tmp

# SYS command. line 417

 /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/utils/gappedpeak.py /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H4ac/out/peak/macs2/overlap/SRR1015998.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.naive_overlap.filt.gappedPeak.tmp /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H4ac/out/peak/macs2/overlap/SRR1015998.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.naive_overlap.filt.gappedPeak.hammock

# SYS command. line 418

 rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H4ac/out/peak/macs2/overlap/SRR1015998.nodup.tagAlign_x_ENCFF001HNC.nodup.tagAlign.naive_overlap.filt.gappedPeak.tmp
 
 
   
--------------------Stdout--------------------
21838 (process ID) old priority 0, new priority 10

  
 		 

    
  
 
  Num   25  
 
  ID   task.graphviz.report.line_97.id_34  
 
  Name   report 
 
  Thread   thread_Root  
 
  PID   23068  
 
 		  
 
  OK   true   
 
  Exit Code   0   
 
  Retries    
 
  State   FINISHED  
 
  Dep.   OK  
 
  Cpus     
 
  Mem    
 
 		  
 
  Start   2017-01-29 01:27:19  
 
  End   2017-01-29 01:27:28  
 
  Elapsed   00:00:09  
 
  Timeout  00:00:-1 
 
  Wall Timeout   100 days 
 
 		  
 
  Input files     
 
  Output files     
 
  Dependencies     
 
 		  
 
# SYS command. line 98

 if [[ -f $(which conda) && $(conda env list | grep aquas_chipseq | wc -l) != "0" ]]; then source activate aquas_chipseq; sleep 5; fi;  export PATH=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/.:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/modules:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/utils:${PATH}:/bin:/usr/bin:/usr/local/bin:${HOME}/.bds; set -o pipefail; STARTTIME=$(date +%s); renice -n 10 $$

# SYS command. line 99

 dot -Tsvg /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H4ac/out/report/H4ac_workflow.dot > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H4ac/out/report/H4ac_workflow.svg 2> /dev/null || echo "svg: /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H4ac/out/report/H4ac_workflow.svg" # to suppress dot font error (exit code=1)
 
 
   
--------------------Stdout--------------------
23073 (process ID) old priority 0, new priority 10

  
 		 

    
  
 
  Num   26  
 
  ID   task.report.pdf2png.line_379.id_39  
 
  Name   pdf2png 
 
  Thread   thread_Root  
 
  PID   23074  
 
 		  
 
  OK   true   
 
  Exit Code   0   
 
  Retries    
 
  State   FINISHED  
 
  Dep.   OK  
 
  Cpus     
 
  Mem    
 
 		  
 
  Start   2017-01-29 01:27:19  
 
  End   2017-01-29 01:27:28  
 
  Elapsed   00:00:08  
 
  Timeout  00:00:-1 
 
  Wall Timeout   100 days 
 
 		  
 
  Input files  /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H4ac/out/qc/rep1/SRR1015998.nodup.15M.cc.plot.pdf
   
 
  Output files   /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H4ac/out/qc/rep1/SRR1015998.nodup.15M.cc.plot.png
  
 
  Dependencies     
 
 		  
 
# SYS command. line 380

 if [[ -f $(which conda) && $(conda env list | grep aquas_chipseq | wc -l) != "0" ]]; then source activate aquas_chipseq; sleep 5; fi;  export PATH=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/.:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/modules:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/utils:${PATH}:/bin:/usr/bin:/usr/local/bin:${HOME}/.bds; set -o pipefail; STARTTIME=$(date +%s); renice -n 10 $$

# SYS command. line 381

 gs -dFirstPage=1 -dLastPage=1 -dTextAlphaBits=4 -dGraphicsAlphaBits=4 -r110x110 \
			-dUseCropBox -dQUIET -dSAFER -dBATCH -dNOPAUSE -dNOPROMPT -sDEVICE=png16m \
			-sOutputFile=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H4ac/out/qc/rep1/SRR1015998.nodup.15M.cc.plot.png \
			-r144 /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H4ac/out/qc/rep1/SRR1015998.nodup.15M.cc.plot.pdf
 
 
   
--------------------Stdout--------------------
23083 (process ID) old priority 0, new priority 10

  
 		 

	






	
 Global scope 

	Note: Global scope when program finished execution.
	

	
  Type  Name  Value  

	
  string  _  /usr/bin/bds  

	
  bool  allowEmpty  false  

	
  string[]  args  [-title, H4ac, -species, hg38, -fastq1, /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/RawReadsFiles/SRR1015998.fastq.gz, -ctl_fastq, /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherHek293Data/ENCFF001HNC.fastq.gz, -final_stage, idr, -histone, $]  

	
  bool  canFail  false  

	
  string  CPATH  /users/imk1/anaconda2/pkgs/gsl-1.16-1/include  

	
  int  cpus  -1  

	
  int  cpusLocal  56  

	
  int  day  86400  

	
  string  DEEPLIFT_DIR  /srv/scratch/imk1/TFBindingPredictionProject/src/deeplift_private/deeplift  

	
  string  DERBY_HOME  /usr/lib/jvm/java-8-oracle/db  

	
  string  DISPLAY  localhost:12.0  

	
  real  E  2.718281828459045  

	
  string  ENHANCER_SCRIPTS_DIR  /srv/scratch/imk1/TFBindingPredictionProject/src/enhancer_prediction_code/  

	
  int  G  1073741824  

	
  string  HOME  /users/imk1/  

	
  int  hour  3600  

	
  string  J2REDIR  /usr/lib/jvm/java-8-oracle/jre  

	
  string  J2SDKDIR  /usr/lib/jvm/java-8-oracle  

	
  string  JAVA_HOME  /usr/lib/jvm/java-8-oracle  

	
  int  K  1024  

	
  string  KERAS_DIR  /users/imk1/.local/lib/python2.7/site-packages/keras/  

	
  string  KRB5CCNAME  FILE:/tmp/krb5cc_1048_mOv3iE  

	
  string  LANG  en_US.UTF-8  

	
  string  LIBRARY_PATH  /users/imk1/anaconda2/pkgs/gsl-1.16-1/lib  

	
  string  LOADEDMODULES    

	
  string  LOGNAME  imk1  

	
  int  M  1048576  

	
  string  MAIL  /var/mail/imk1  

	
  int  mem  -1  

	
  int  minute  60  

	
  string  MODULE_VERSION  3.2.10  

	
  string  MODULE_VERSION_STACK  3.2.10  

	
  string  MODULEPATH  /usr/local/Modules/versions\t\t\t\t:/usr/local/Modules/$MODULE_VERSION/modulefiles\t:/modules/\t\t\t\t:/software/modulefiles  

	
  string  MODULESHOME  /software/env_module/3.2.10  

	
  string  NLSPATH  /usr/dt/lib/nls/msg/%L/%N.cat  

	
  string  node    

	
  int  P  1125899906842624  

	
  string  PATH  /users/imk1/anaconda2/bin:/users/imk1/perl5/bin:/srv/scratch/imk1/TFBindingPredictionProject/src/bedtools2/bin:/usr/local/cuda/bin:/srv/scratch/imk1/TFBindingPredictionProject/src/rcade/:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games:/snap/bin:/software/miniconda3/bin:/usr/lib/jvm/java-8-oracle/bin:/usr/lib/jvm/java-8-oracle/db/bin:/usr/lib/jvm/java-8-oracle/jre/bin:/users/imk1/edirect:/users/imk1/edirect  

	
  string  PERL5LIB  /users/imk1/perl5/lib/perl5  

	
  string  PERL_LOCAL_LIB_ROOT  /users/imk1/perl5  

	
  string  PERL_MB_OPT  --install_base \"/users/imk1/perl5\"  

	
  string  PERL_MM_OPT  INSTALL_BASE=/users/imk1/perl5  

	
  real  PI  3.141592653589793  

	
  string  ppwd  /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H4ac  

	
  string  programName  chipseq.bds  

	
  string  programPath  /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/chipseq.bds  

	
  string  PWD  /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/Liu2013Data/H4ac  

	
  string  PYTHONPATH  /users/imk1/.local/lib/python2.7/site-packages/keras/:/srv/scratch/imk1/TFBindingPredictionProject/src/pybedtools/  

	
  string  queue    

	
  int  retry  0  

	
  string  RULEFITBASE  /srv/scratch/imk1/TFBindingPredictionProject/src/RuleFit/  

	
  string  SHELL  /bin/bash  

	
  string  SHLVL  3  

	
  string  SSH_CLIENT  171.65.77.8 32974 22  

	
  string  SSH_CONNECTION  171.65.77.8 32974 171.65.76.63 22  

	
  string  SSH_TTY  /dev/pts/4  

	
  string  STY  13605.H4ac.BDS  

	
  string  system  sge  

	
  int  T  1099511627776  

	
  string  TERM  screen  

	
  string  TERMCAP  SC|screen|VT 100/ANSI X3.64 virtual terminal:\\\n\t:DO=\\E[%dB:LE=\\E[%dD:RI=\\E[%dC:UP=\\E[%dA:bs:bt=\\E[Z:\\\n\t:cd=\\E[J:ce=\\E[K:cl=\\E[H\\E[J:cm=\\E[%i%d;%dH:ct=\\E[3g:\\\n\t:do=^J:nd=\\E[C:pt:rc=\\E8:rs=\\Ec:sc=\\E7:st=\\EH:up=\\EM:\\\n\t:le=^H:bl=^G:cr=^M:it#8:ho=\\E[H:nw=\\EE:ta=^I:is=\\E)0:\\\n\t:li#24:co#80:am:xn:xv:LP:sr=\\EM:al=\\E[L:AL=\\E[%dL:\\\n\t:cs=\\E[%i%d;%dr:dl=\\E[M:DL=\\E[%dM:dc=\\E[P:DC=\\E[%dP:\\\n\t:im=\\E[4h:ei=\\E[4l:mi:IC=\\E[%d@:ks=\\E[?1h\\E=:\\\n\t:ke=\\E[?1l\\E>:vi=\\E[?25l:ve=\\E[34h\\E[?25h:vs=\\E[34l:\\\n\t:ti=\\E[?1049h:te=\\E[?1049l:Km=\\E[M:k0=\\E[10~:k1=\\EOP:\\\n\t:k2=\\EOQ:k3=\\EOR:k4=\\EOS:k5=\\E[15~:k6=\\E[17~:k7=\\E[18~:\\\n\t:k8=\\E[19~:k9=\\E[20~:k;=\\E[21~:F1=\\E[23~:F2=\\E[24~:\\\n\t:kh=\\E[1~:@1=\\E[1~:kH=\\E[4~:@7=\\E[4~:kN=\\E[6~:kP=\\E[5~:\\\n\t:kI=\\E[2~:kD=\\E[3~:ku=\\EOA:kd=\\EOB:kr=\\EOC:kl=\\EOD:  

	
  int  timeout  -1  

	
  string  USER  imk1  

	
  string  UTIL_SCRIPTS_DIR  /srv/scratch/imk1/TFBindingPredictionProject/src/av_scripts/  

	
  int  walltimeout  8640000  

	
  int  week  604800  

	
  string  WINDOW  0  

	
  string  XDG_RUNTIME_DIR  /run/user/1048  

	
  string  XDG_SESSION_ID  45170  

	
  string  XFILESEARCHPATH  /usr/dt/app-defaults/%L/Dt